Bhardwaj, A, Banh, R. S., Zhang, W., Sidhu, S. S. & Neel, B. G. (2022). MMD-associated RNF213 SNPs encode dominant-negative alleles that globally impair ubiquitylation. Life Sci. Alliance 5, e202000807.
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Veggiani, G., Yates, B. P., Martyn, G. D., Manczyk, N., Singer, A. U., Kurinov, I., Sicheri, F. & Sidhu, S. S. (2022). Panel of engineered ubiquitin variants targeting the family of human ubiquitin interacting motifs. ACS Chem Biol. 17, 941-56.
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Mishra, N., Teyra, J., Boytz, R., Miersch, S., Merritt, T. N., Cardarelli, L., Gorelik, M., Mihalic, F., Jemth, P., Davey, R., Sidhu, S. S., Leung, D. W. & Amarasinghe, G. K. (2022) Development of monoclonal antibodies to detect for SARS-CoV-2 proteins. J. Mol. Biol. 434, 167583.
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Spitalieri, P., Centofanti, F., Murdocca, M., Scioli, M. G., Latini, A., Di Cesare, S., Citro, G., Rossi, A., Orlandi, A., Miersch, S., Sidhu, S. S., Pandolfi, P. P., Botta, A., Sangiuolo, F. & Novelli, G. (2022). Two different therapeutic approaches for SARS-CoV-2 in hiPSCs-derived lung organoids. Cells 11, 1235.
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Sankar, K., Trainor, K., Blazer, L. L., Adams, J. J., Sidhu, S. S., Day, T., Meiering, E. & Maier, J. K. X. (2022). A descriptor set for quantitative structure-property relationship prediction in biologics. Mol. Inform. [Mar 11 Epub ahead of print].
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Chrustowicz, J., Sherpa, D., Teyra, J., Siong Loke, M., Popowicz, G., Basquin, J., Sattler, M., Rajan Prabu, J., Sidhu, S. S. & Schulman, B. A. (2021). Multifaceted N-degron recognition and ubiquitylation by GID/CTLH E3 ligases. J. Mol. Biol. 434, 167347.
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Philpott, D. N., Gomis, S., Wang, H., Atwal, R., Kelil, A., Sack, T., Morningstar, B., Burnie, C., Sargent, E. H., Angers, S., Sidhu, S. S. & Kelley, S. O. (2021). Rapid on-cell selection of high-performance human antibodies. ACS Cent. Sci. 26, 102-9.
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Ma, Y., Chen, K., Xia, F., Atwal, R., Wang, H., Ahmed, S. U., Cardarelli, L., Lui, I., Duong, B., Wang, Z., Wells, J. A., Sidhu, S. S. & Kelley S. O. (2021). Phage-based profiling of rare single cells using nanoparticle-directed capture. ACS Nano. 15, 19202-10.
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Tang, J. Q., Veggiani, G., Singer, A., Teyra, J., Chung, J. & Sidhu, S. S. (2021). A panel of engineered ubiquitin variants targeting the family of domains found in ubiquitin specific proteases (DUSPs). J. Mol. Biol. 433, 167300.
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Linossi, E. M., Li, K., Veggiani, G., Tan, C., Dehkhoda, F., Hockings, C., Calleja, D., Keating, N., Feltham, R., Brooks, A., Li, S. S., Sidhu, S. S., Babon, J. J., Kershaw, N. J. & Nicholson, S. E. (2021). Discovery of an exosite on the SOCS2-SH2 domain that enhances SH2 binding to phosphorylated ligands. Nat. Commun. 12, 7032.
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Luz, D., Gómez, F. D., Ferreira, R. L., Melo, B. S., Guth, B. E. C., Quintilio, W., Moro, A. M., Presta, A., Sacerdoti, F., Ibarra, C., Chen, G., Sidhu, S. S., Amaral, M. M. & Piazza, R. M. F. (2021). The deleterious effects of Shiga toxin type 2 are neutralized in vitro by FabF8:Stx2 recombinant monoclonal antibody. Toxins. 13, 825.
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Nilvebrant, J., Ereño-Orbea, J., Gorelik, M., Julian, M. C., Tessier, P. M., Julien, J. P., & Sidhu, S. S. (2021). Systematic engineering of optimized autonomous heavy-chain variable domains. J. Mol. Biol. 433, 167241.
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Phillips, A. T., Boumil, E. F., Castro, N., Venkatesan, A., Gallo, E., Adams, J. J., Sidhu, S. S. & Bernstein, A. M. (2021). USP10 promotes fibronectin recycling, secretion, and organization. Invest. Ophthalmol. Vis. Sci. 62, 15.
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Ganaie, S. S., Schwarz, M. M., McMillen, C. M., Price, D. A., Feng, A. X., Albe, J. R., Wang, W., Miersch, S., Orvedahl, A., Cole, A. R., Sentmanat, M. F., Mishra, N., Boyles, D. A., Koenig, Z. T., Kujawa, M. R., Demers, M. A., Hoehl, R. M., Moyle, A. B., Wagner, N. D., Stubbs, S. H., Cardarelli, L., Teyra, J., McElroy, A., Gross, M. L., Whelan, S. P. J., Doench, J., Cui, X., Brett, T. J., Sidhu, S. S., Virgin, H. W., Egawa, T., Leung, D. W., Amarasinghe, G. K. & Hartman, A. L. (2021). Lrp1 is a host entry factor for Rift Valley fever virus. Cell 184, 5163-78.
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Middleton, A. J., Teyra, J., Zhu, J., Sidhu, S. S. & Day, C. L. (2021). Identification of ubiquitin variants that inhibit the E2 ubiquitin conjugating enzyme, Ube2k. ACS Chem. Biol. 16, 1745-56.
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Miersch, S., Li, Z., Saberianfar, R., Ustav, M., Case, J. B., Blazer, L., Chen, C., Ye, W., Pavlenco, A., Gorelik, M., Garcia Perez, J., Subramania, S., Singh, S., Ploder, L., Ganaie, S., Chen, R. E., Leung, D. W., Pandolfi, P. P., Novelli, G., Matusali, G., Colavita, F., Capobianchi, M. R., Jain, S., Gupta, J. B., Amarasinghe, G. K., Diamond, M. S., Rini, J. & Sidhu, S. S. (2021). Tetravalent SARS-CoV-2 neutralizing antibodies show enhanced potency and resistance to escape mutations. J. Mol. Biol. 433, 167177.
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Teyra, J., McLaughlin, M., Singer, A., Kelil, A., Ernst, A., Sicheri, F. & Sidhu, S. S. (2021).
Comprehensive assessment of the relationship between site-2 specificity and helix α2 in the erbin PDZ domain. J. Mol. Biol. 433, 167115.
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Murdocca, M., Citro, G., Romeo, I., Lupia, A., Miersch, S., Amadio, B., Bonomo, A., Rossi, A., Sidhu, S. S., Pandolfi, P. P., Alcaro, S., Sangiuolo, F. C. & Novelli, G. (2021). Peptide platform as a powerful tool in the fight against COVID-19. Viruses 13, 1667.
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Gallo, E., Kelil, A., Haughey, M., Cazares-Olivera, M., Yates, B. P., Zhang, M., Wang, N. Y., Blazer, L., Carderelli, L., Adams, J. J., Kossiakoff, A. A., Wells, J. A., Xie, W., & Sidhu, S. S. (2021). Inhibition of cancer cell adhesion, migration and proliferation by a bispecific antibody that targets two distinct epitopes on αv integrins. J. Mol. Biol. 433, 167090.
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Chidiac, R., Abedin, M., Macleod, G., Yang, A., Thibeault, P. E., Blazer, L. L., Adams, J. J., Zhang, L., Roehrich, H., Jo, H. N., Seshagiri, S., Sidhu, S. S., Junge, H. J. & Angers, S. (2021). A Norrin/Wnt surrogate antibody stimulates endothelial cell barrier function and rescues retinopathy. EMBO Mol. Med. 13, e13977.
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Le, P. J., Miersch, S., Forbes, M. W., Jarvik, N., Ku, A., Sidhu, S. S., Reilly, R. M. & Winnik, M. A. (2021). Site-specific conjugation of metal-chelating polymers to anti-frizzled-2 antibodies via microbial transglutaminase. Biomacromolecules 22, 2491-504.
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Kelil, A., Gallo, E., Banerjee, S., Adams, J. J. & Sidhu, S. S. (2021). CellectSeq: In silico discovery of antibodies targeting integral membrane proteins combining in situ selections and next-generation sequencing. Commun. Biol. 4, 561.
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Choe, J. H., Watchmaker, P. B., Simic, M. S., Gilbert, R. D., Li, A. W., Krasnow, N. A., Downey, K. M., Yu, W., Carrera, D. A., Celli, A., Cho, J., Briones, J. D., Duecker, J. M., Goretsky, Y. E., Dannenfelser, R., Cardarelli, L., Troyanskaya, O., Sidhu, S., Roybal, K. T., Okada, H. & Lim, W. A. (2021). SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma. Sci. Transl. Med. 13, eabe7378.
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Suryamohan, K., Diwanji, D., Stawiski, E. W., Gupta, R., Miersch, S., Liu, J., Chen, C., Jiang, Y.-P., Fellouse, F. A., Sathirapongsasuti, J. F., Albers, P. K., Deepak, T., Saberianfar, R., Ratan, A., Washburn, G., Mis, M., Santhosh, D., Somasekar, S., Hiranjith, G. H., Vargas, D., Mohan, S., Phalke, S., Kuriakose, B., Antony, A., Ustav, M., Schuster, S. C., Sidhu, S., Junutula, J. R., Jura, N., Seshagiri, S. (2021). Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2. Commun. Biol. 4, 475.
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Novelli, G., Liu, J., Biancolella, M., Alonzi, T., Novelli, A., Patten, J. J., Cocciadiferro, D., Agolini, E., Colona, V. L., Rizzacasa, B., Giannini, R., Bigio, B., Goletti, D., Capobianchi, M. R., Grelli, S., Mann, J., McKee, T. D., Cheng, K., Amanat, F., Krammer, F., Guarracino, A., Pepe, G., Tomino, C., Tandjaoui-Lambiotte, Y., Uzunhan, Y., Tubiana, S., Ghosn, J.; COVID Human Genetic Effort; French COVID Cohort Study Group; CoV-Contact Cohort; Notarangelo, L. D., Su, H. C., Abel, L., Cobat, A., Elhanan, G., Grzymski, J. J., Latini, A., Sidhu, S. S., Jain, S., Davey, R. A., Casanova, J. L., Wei, W. & Pandolfi, P. P. (2021). Inhibition of HECT E3 ligases as potential therapy for COVID-19. Cell Death Dis. 12, 310.
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Marinec, P. S., Landgraf, K. E., Uppalapati, M., Chen, G., Xie, D., Jiang, Q., Zhao, Y., Petriello, A., Deshayes, K., Kent, S. B., H., Ault-Riche, D. & Sidhu, S. S. (2021). A non-immunogenic bivalent d-protein potently inhibits retinal vascularization and tumor growth. ACS Chem. Biol. 16, 548-56.
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Zeitler, L., Fiore , A., Meyer, C., Russier, M., Zanella, G., Suppmann, S., Gagaro, M., Sidhu, S. S., Seshagiri, S., Ohnmacht, C., Köcher, T., Fallarino, F., Linkermann, A. & Murray, P. J. (2021). Anti-ferroptotic mechanism of IL4i1-mediated amino acid metabolism. eLife 10, e64806.
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Liang, J., Ruthel, G., Sagum, C. A., Bedford, M. T., Sidhu, S. S., Sudol, M., Jaladanki, C. K., Fan, H., Freedman, B. D. & Harty, R. N. (2021). Angiomotin counteracts the negative regulatory effect of host WWOX on viral PPxY-mediated egress. J. Virol. 95, e00121-21.
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Enderle, L., Shalaby, K. H., Gorelik, M., Weiss, A., Blazer, L. L., Paduch, M., Cardarelli, L., Kossiakoff, A., Adams, J. J. & Sidhu, S. S. (2021). A T cell redirection platform for co-targeting dual antigens on solid tumors. MAbs 13, 1933690.
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Teyra, J., Kelil, A., Jain, S., Helmy, M., Jajodia, R., Hooda, Y., Gu, J. D’Cruz, A. A., Nicholson, S. E., Min, J., Sudol, M., Kim, P. M., Bader, G. D. & Sidhu, S. S. (2020). Large-scale survey and database of high affinity ligands for peptide recognition modules. Mol. Syst. Biol. 16, e9310.
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Maculins, T., Garcia-Pardo, J., Skenderovic, A., Gebel, J., Putyrski, M., Vorobyov, A., Busse, P., Varga, G., Kuzikov, M., Zaliani, A., Rahighi, S., Schaeffer, V., Parnham, M. J., Sidhu, S. S., Ernst, A., Dötsch, V., Akutsu, M. & Dikic, I. (2020). Discovery of protein-protein interaction inhibitors by integrating protein engineering and chemical screening platforms. (2020). Cell Chem. Biol. 27, 1441-51.
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Yuan, X., Garg, S., De Haan, K., Fellouse, F. A., Gopalsamy, A., Tykvart, J., Sidhu, S. S., Verma, M. M., Pal, P., Hillan, E., Dou, J. J. & Aitchison, J. S. (2020). Bead-based multiplex detection of dengue biomarkers in a portable imaging device. Biomed. Opt. Express 11, 6154-67.
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Hanna, R., Cardarelli, L., Patel, N., Blazer, L. L., Adams, J. J. & Sidhu, S. S. (2020). A phage-displayed single-chain Fab library optimized for rapid production of single-chain IgGs. Prot. Science 29, 2075-84.
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Case, J. B., Rothlauf, P. W., Chen, R. E., Liu, Z., Zhao, H., Kim, A. S., Bloyet, L.-M., Zeng, Q., Tahan, S., Droit, L., Ilagan, M. X. G., Tartell, M. A., Amarasinghe, G., Henderson, J. P., Miersch, S., Ustav, M., Sidhu, S., Virgin, H. W., Wang, D., Ding, S., Corti, D., Theel, E. S., Fremont, D., Diamond, M. S., Whelan, S. P. J. (2020). Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. Cell Host Microbe 28, 475-485.e5.
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Neyra, J. A., Moe, O. W., Pastor, J., Gianella, F., Sidhu, S. S., Sarnak, M. J., Ix, J. H. & Drew, D. A. (2020). Performance of soluble Klotho assays in clinical samples of kidney disease. Clin. Kidney J. 13, 235-244.
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Laver, J. D., Ly, J., Winn, A. K., Karaiskakis, A., Lin, S., Nie, K., Benic, G., Jaberi-Lashkari, N., Cao, W. X., Khademi, A., Westwood, J. T., Sidhu, S. S., Morris, Q., Angers, S., Smibert, C. A. & Lipshitz, H. D. (2020). The RNA-binding protein Rasputin/G3BP enhances the stability and translation of its target mRNAs. Cell Rep. 30, 3353-67.
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Garg, P., Ceccarelli, D. F., Keszei, A. F., Kourinov, I., Sicheri, F. & Sidhu, S. S. (2019). Structural and functional analysis of ubiquitin-based inhibitors that target the backsides of E2 enzymes. J. Mol. Biol. 432, 952-66.
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Liu, S., Miersch, S., Li, P., Bai, B., Liu, C., Qin, W., Su, J., Huang, H., Pan, J., Sidhu, S. S. & Wu, D. (2020). A synthetic human antibody antagonizes IL-18Rβ signaling through an allosteric mechanism. J. Mol. Biol. 432, 1169-82.
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Teyra, J., Ernst, A., Singer, A., Sicheri, F. & Sidhu, S. S. (2020). Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities. Protein Sci. 29:433–42.
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Stiffler, M. A., Poelwijk, F. J., Brock, K. P., Stein, R. R., Riesselman, A., Teyra, J., Sidhu, S. S., Marks, D. S., Gauthier, N. P. & Sander, C. (2020). Protein structure from experimental evolution. Cell Syst. 10, 15-24.
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Han, Z., Dash, S., Sagum, C. A., Ruthel, G., Jaladanki, C. K., Berry, C. T., Schwoerer, M. P., Harty, N. M., Freedman, B. D., Bedford, M. T., Fan, H., Sidhu, S. S., Sudol, M., Shtanko, O. & Harty, R. N. (2020). Modular mimicry and engagement of the Hippo pathway by Marburg virus VP40: Implications for filovirus biology and budding. PLoS Pathog. 16, e1008231.
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Gallo, E., Kelil, A., Bayliss, P. E., Jeganathan, A., Egorova, O., Ploder, L., Adams, J. A., Giblin, P. & Sidhu, S. S. (2020). In situ antibody phage display yields optimal inhibitors of integrin α11/β1. MAbs 12, 1717265.
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Zhang, Y., Sun, X., Qian, Y., Yi, H., Song, K., Zhu, H., Zonta, F., Chen, W., Ji, Q., Miersch, S., Sidhu, S. S. & Wu, D. (2019). A potent anti-SpuE antibody allosterically inhibits type III secretion system and attenuates virulence of Pseudomonas aeruginosa. J. Mol. Biol. 431, 4882-96.
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Chen, G., Karauzum, H., Long, H., Carranza, D., Holtsberg, F. W., Howell, K. A., Abaandou, L., Zhang, B., Jarvik, N., Ye, W., Liao, G. C., Gross, M. L., Leung, D. W., Amarasinghe, G. K., Aman, M. J. & Sidhu, S. S. (2019) Potent neutralization of staphylococcal enterotoxin B in vivo by antibodies that block binding to the T-cell receptor. J. Mol. Biol. 431, 4354-67.
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Gabrielsen, M., Buetow, L., Kowalczyk, D., Zhang, W., Sidhu, S. S. & Huang, D. T. (2019) Identification and characterization of mutations in ubiquitin required for non-covalent dimer formation. Structure 27, 1452-9.
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Watson, E. R., Grace, C. R. R., Zhang, W., Miller, D. J., Davidson, I. F., Prabu, J. R., Yu, S., Bolhuis, D. L., Kulko, E. T., Vollrath, R., Haselbach, D., Stark, H., Peters, J. M., Brown, N. G., Sidhu, S. S. & Schulman B.A. (2019) Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Proc. Natl. Acad. Sci. USA 116, 17280-9.
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Tao, Y., Mis, M., Blazer, L., Ustav Jr, M., Steinhart, Z., Chidiac, R., Kubarakos, K., O’Brien, S., Wang, X., Jarvik, N., Patel, N., Adams, J., Moffat, J., Angers, S. & Sidhu, S. S. (2019) Tailored tetravalent antibodies potently and specifically activate Wnt/Frizzled pathways in cells, organoids and mice. eLIFE 8, e46134.
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Amatya, P., Wagner, N., Chen, G., Luthra, P., Shi, L., Borek, D., Pavlenco, A., Rohrs, H. W., Basler, C. F., Sidhu, S. S., Gross, M. L. & Leung, D. W. (2019) Inhibition of Marburg virus RNA synthesis by a synthetic anti-VP35 antibody. ACS Infect. Dis. 5, 1385-96.
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Chen, G., Cook, J. D., Ye, W., Lee, J. E. & Sidhu, S. S. (2019) Optimization of peptidic HIV-1 fusion inhibitor T20 by phage display. Protein Sci. 28, 1501-12.
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Veggiani, G., Gerpe, M. C. R., Sidhu, S. S. & Zhang, W. (2019) Emerging drug development technologies targeting ubiquitination for cancer therapeutics. Pharmacol. Ther. 199, 139-54.
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Manczyk, N., Veggiani, G., Gish, G. D., Yates, B. P., Ernst, A., Sidhu, S. S. & Sicheri F. (2019) Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif. Protein Sci. 28, 848-56.
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Lam, A. J., MacDonald, K. N., Pesenacker, A. M., Juvet, S. C., Morishita, K. A., Bressler, B.; iGenoMed Consortium, Pan, J. G., Sidhu, S. S., Rioux, J. D. & Levings, M. K. (2019) Innate control of tissue-reparative human regulatory T cells. J. Immunol. 202, 2195-209.
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Teyra, J., Singer, A. U., Schmitges, F. W., Jaynes, P., Kit Leng Lui, S., Polyak, M. J., Fodil, N., Krieger, J. R., Tong, J., Schwerdtfeger, C., Brasher, B. B., Ceccarelli, D. F. J., Moffat, J., Sicheri, F., Moran, M. F., Gros, P., Eichhorn, P. J. A., Lenter, M., Boehmelt, G. Sidhu, S. S. (2019) Structural and functional characterization of ubiquitin variant inhibitors of USP15. Structure 27, 590-605.
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Raman, S., Beilschmidt, M., To, M., Lin, K., Lui, F., Jmeian, Y., Ng, M., Fernandez, M., Fu, Y., Mascall, K., Duque, A., Wang, X., Pan, G., Angers, S., Moffat, J., Sidhu, S. S., Magram, J., Sinclair, A. M., Fransson, J. & Julien, J. P. (2019) Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies. Proc. Natl. Acad. Sci. USA 116, 6812-17.
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Pascoe, N., Seetharaman, A., Teyra, J., Manczyk, N., Satori, M. A., Tjandra, D., Makhnevych, T., Schwerdtfeger, C., Brasher, B. B., Moffat, J., Costanzo, M., Boone, C., Sicheri, F. & Sidhu, S. S. (2019) Yeast two-hybrid analysis for ubiquitin-variant inhibitors of human deubiquitinases. J. Mol. Biol. 431, 1160-71.
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Manczyk, N., Veggiani, G., Teyra, J., Strilchuk, A. W., Sidhu, S. S. & Sicheri, F. (2019) The ubiquitin interacting motifs of USP37 act on the proximal Ub of a di-Ub chain to enhance catalytic efficiency. Sci. Rep. 9, 4119.
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Liu, H., Huang, H., Voss, C., Kaneko, T., Qin, W., Sidhu, S. S. & Li, S. S-C. (2018) Surface loops in a single SH2 domain are capable of encoding the spectrum of specificity of the SH2 family. Mol. Cell. Proteomics 18, 372-82.
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Veggiani, G., Huang, H., Yates, B., Tong, J., Kaneko, T., Joshi, R., Li, S. S., Moran, M. F., Gish, G. & Sidhu, S. S. (2019) Engineered SH2 domains with tailored specificities and enhanced affinities for phosphoproteome analysis. Protein Sci. 28, 403-13.
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Nixon, A. M. L., Duque, A., Yelle, N., McLaughlin, M., Davoudi, S., Pedley, N. M., Haynes, J., Brown, K. R., Pan, J., Hart, T., Gilbert, P. M., Singh, S. K., O'Brien, C. A., Sidhu, S. S. & Moffat, J. (2019) A rapid in vitro methodology for simultaneous target discovery and antibody generation against functional cell subpopulations. Sci. Rep. 9, 842.
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Turowec, J. P., Lau, E. W. T., Wang, X., Brown, K. R., Fellouse, F. A., Jawanda, K. K., Pan, J., Moffat, J. & Sidhu, S. S. (2018) Functional genomic characterization of a synthetic anti-HER3 antibody reveals a role for ubiquitination by RNF41 in the anti-proliferative response. J. Biol. Chem. 294, 1396-1409.
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Ben-David, M., Huang, H., Sun, M. G. F., Corbi-Verge, C., Petsalaki, E., Liu, K., Gfeller, D., Garg, P., Tempel, W., Sochirca, I., Shifman, J. M., Davidson, A., Min, J., Kim, P. M. & Sidhu, S. S. (2019) Allosteric modulation of binding specificity by alternative packing of protein cores. J. Mol. Biol. 431, 336-50.
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Hu, A. X., Adams, J. J., Vora, P., Qazi, M., Singh, S. K., Moffat, J. & Sidhu, S. S. (2019) EPH profiling of BTIC populations in glioblastoma multiforme using CyTOF. Methods Mol. Biol. 1869, 155-68.
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Newsted, D., Banerjee, B., Watt, K., Nersesian, S., Truesdell, P., Blazer, L. L., Cardarelli, L., Adams, J. J., Sidhu, S. S. & Craig, A. W. (2019) Blockade of TGF-β signaling with novel synthetic antibodies limits immune exclusion and improves chemotherapy response in metastatic ovarian cancer models. Oncoimmunology 8, e1539613.
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Kini, R. M., Sidhu, S. S. & Laustsen, A. H. (2018) Biosynthetic Oligoclonal Antivenom (BOA) for snakebite and next-generation treatments for snakebite victims. Toxins 10, 534-43.
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Jangra, R. K., Herbert, A. S., Li, R., Jae, L. T., Kleinfelter, L. M., Slough, M. M., Barker, S. L., Guardado-Calvo, P., Román-Sosa, G., Dieterle, M. E., Kuehne, A. I., Muena, N. A., Wirchnianski, A. S., Nyakatura, E. K., Fels, J. M., Ng, M., Mittler, E., Pan, J., Bharrhan, S., Wec, A. Z., Lai, J. R., Sidhu, S. S., Tischler, N. D., Rey, F. A., Moffat, J., Brummelkamp, T. R., Wang, Z., Dye, J. M. & Chandran, K. (2018) Protocadherin-1 is essential for cell entry by New World hantaviruses. Nature 563, 559-563.
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Park, M., Xu, X., Min, W., Sugiman-Marangos, S. N., Beilhartz, G. L., Adams, J. J., Sidhu, S. S., Grunebaum, E. & Melnyk, R. A. (2018) Intracellular delivery of human purine nucleoside phosphorylase by engineered diphtheria toxin rescues function in target cells. Mol. Pharm. 15, 5217-26.
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Pavlovic, Z., Adams, J. J., Blazer, L. L., Gakhal, A. K., Jarvik, N., Steinhart, Z., Robitaille, M., Mascall, K., Pan, J., Angers, S., Moffat, J. & Sidhu, S. S. (2018) A synthetic anti-Frizzled antibody engineered for broadened specificity exhibits enhanced anti-tumor properties. MAbs 10, 1157-67.
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Gorelik, M., Manczyk, N., Pavlenco, A., Kurinov, I., Sidhu, S. S. & Sicheri, F. (2018) A structure-based strategy for engineering selective ubiquitin variant inhibitors of Skp1-Cul1-F-box ubiquitin ligases. Structure 26, 1226-36.
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Qazi, M. A., Vora, P., Venugopal, C., Adams, J., Singh, M., Hu, A. X., Gorelik, M., Subapanditha, M. K., Savage, N., Yang, J., Chokshi, C., London, M., Gont, A., Bobrowski, D., Grinshtein, N., Brown, K. R., Murty, N. K., Nilvebrant, J., Kaplan, D. R., Moffat, J., Sidhu, S. S. & Singh, S. K. (2018) Co-targeting ephrin receptor tyrosine kinases A2 and A3 in cancer stem cells reduces growth of recurrent glioblastoma. Cancer Res. 78, 5023-37.
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Han, Z., Schwoerer, M. P., Hicks, P., Liang, J., Ruthel, G., Berry, C. T., Freedman, B. D., Sagum, C. A., Bedford, M. T., Sidhu, S. S., Sudol, M. & Harty, R. N. (2018) Host protein BAG3 is a negative regulator of Lassa VLP egress. Diseases 6, E64.
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Veggiani, G. & Sidhu, S. S. (2018) Peptides meet ubiquitin: simple interactions regulating complex cell signalling. Peptide Science 111, e24091.
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Nelson, B., Adams, J., Kuglstatter, A., Li, Z., Harris, S. F., Liu, Y., Bohini, S., Ma, H., Klumpp, K., Gao, J. & Sidhu, S. S. (2018) Structure-guided combinatorial engineering facilitates affinity and specificity optimization of anti-CD81 antibodies. J. Mol. Biol. 430, 2139-52.
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Huang, G., Zhong, Z., Miersch, S., Sidhu, S. S., S. S., Hou, S.-C. & Wu, D. (2018) Construction of synthetic phage displayed Fab library with tailored diversity. J. Vis. Exp. 135, e57357.
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Ordureau, A., Paulo, J., Zhang, W., Ahfeldt, T., Zhang, J., Heo, J., Rubin, L., Sidhu, S. S., Gygi, S. P. & Harper, J. W. (2018) Dynamics of PARKIN-dependent mitochondrial ubiquitylation in induced neurons and model systems revealed by digital snapshot proteomics. Mol. Cell 70, 1-17.
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Shi, M., Flores, B., Li, P., Gillings, N., McMillan, K. L., Ye, J., Huang, L. J., Sidhu, S. S., Zhong, Y.-P., Grompe, M. T., Streeter, P. R., Moe O. W. & Hu, M. C. (2018) Effects of erythropoietin receptor activity on angiogenesis, tubular injury and fibrosis in acute kidney injury: a "U-shaped" relationship. Am. J. Physiol. Renal Physiol. 314, F501-16.
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Pollock, S. B., Hu, A., Mou, Y., Martinko, A. J., Julien, O., Hornsby, M., Ploder, L., Adams, J. J., Geng, H., Müschen, M., Sidhu, S. S., Moffat, J. & Wells, J. A. (2018) Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies. Proc. Natl. Acad. Sci. USA. 115, 2836-41.
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Luz, D., Shiga, E. A., Chen, G., Quintilio, W., Andrade, F. B., Maranhao, A. Q., Caetano, B. A., Mitsunari, T., Silva, M. A., Rocha, L. B., Moro, A. M., Sidhu, S. S.& Piazza, R. M. F. (2018) The modification in the Stx1 engineering monoclonal antibody structure improves its functionality as diagnostic tool for a rapid latex agglutination test. Antibodies 7, 9.
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Zhang, W. & Sidhu, S. S. (2018) Drug development: Allosteric inhibitors hit USP7 hard (News & Views). Nat. Chem. Biol. 14, 110-11.
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Saxena, A., Bai, B., Hou, S. C., Jiang, L., Ying, T., Miersch, S., Sidhu, S. S. & Wu, D. (2018) Fc Engineering: Tailored Synthetic Human IgG1-Fc Repertoire for High-Affinity Interaction with FcRn at pH 6.0. Methods Mol. Biol. 1827, 399-417.
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Zhang, W. & Sidhu, S. S. (2018) Generating intracellular modulators of E3 ligases and deubiquitinases from phage-displayed ubiquitin variant libraries. Methods Mol. Biol. 1844, 101-19.
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Canny, M. D., Moatti, N., Wan, L. C. K., Fradet-Turcotte, A., Krasner, D., Mateos-Gomez, P. A., Zimmermann, M., Orthwein, A., Juang, Y. C., Zhang, W., Noordermeer, S. M., Seclen, E., Wilson, M. D., Vorobyov, A., Munro, M., Ernst, A., Ng, T. F., Cho, T., Cannon, P. M., Sidhu, S. S., Sicheri, F. & Durocher. D. (2018) Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency. Nat. Biotechnol. 36, 95-102.
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Nilvebrandt, J. & Sidhu, S. S. (2018) Construction of synthetic antibody phage-display libraries. Methods Mol. Biol. 1701, 45-60.
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Chen, G., Sidhu, S. S. & Nilvebrant, J. (2017) Synthetic antibodies in infectious disease. Adv. Exp. Med. Biol. 1053, 79-98.
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Zhang, H., Liu, K., Izumi, N., Huang, H., Ding, D., Ni, Z., Sidhu, S. S., Chen, C., Tomari, Y. & Min, J. (2017) Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2. Proc. Natl. Acad. Sci. USA 114, 12483-88.
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Rissland, O. S., Subtelny, A. O., Wang, M., Lugowski, A., Nicholson, B., Laver, J. D., Sidhu, S. S., Smibert, C. A., Lipshitz, H. D. & Bartel, D. P. (2017) The influence of microRNAs and poly(A) tail length on endogenous mRNA-protein complexes. Genome Biol. 18, 211.
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Gabrielsen, M., Buetow, L., Nakasone, M. A., Ahmed, S. F., Sibbet, G. J., Smith, B. O., Zhang, W., Sidhu, S. S. & Huang, D. T. (2017) A general strategy for discovery of inhibitors and activators of RING and U-box E3 ligases with ubiquitin variants. Mol. Cell 68, 456-70.
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Ghosh, E., Srivastava. A., Baidya, M., Kumari, P., Dwivedi, H., Nidhi, K., Ranjan, R., Dogra, S., Koide, A., Yadav, P. M., Sidhu, S. S., Koide, S. & Shukla, A. K. (2017) A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis. Nat. Nanotechnol. 12, 1190-98.
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Miersch, S., Kuruganti, S., Walter, M. R. & Sidhu, S. S. (2017) A panel of synthetic antibodies that selectively recognize and antagonize members of the interferon alpha family. Protein Eng. Des. Sel. 30, 697-704.
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Teyra, J., Huang, H., Jain, S., Guan, X., Dong, A., Liu, Y., Tempel, W., Min, J., Tong, Y., Kim, P. M., Bader, G. D. & Sidhu, S. S. (2017) Comprehensive analysis of the human SH3 domain family reveals a wide variety of non-canonical specificities. Structure 25, 1598-1610.
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Han, Z., Sagum, C. A., Takizawa, F., Ruthel, G., Berry, C. T., Kong, J., Sunyer, J. O., Freedman, B. D., Bedford, M. T., Sidhu, S. S., Sudol, M. & Harty, R. N. (2017) Ubiquitin Ligase WWP1 Interacts with Ebola Virus VP40 to Regulate Egress. J. Virol. 91, e00812-17.
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Zhang, W., Ben-David, M. & Sidhu, S. S. (2017) Engineering cell signaling modulators from native protein-protein interactions. Curr. Opin.
Struct. Biol. 45, 25-35.
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Apel, A. R., Hoban, K., Chuartzman, S., Tonikian, R., Sidhu, S. S., Schuldiner, M., Wendland, B. & Prosser, D. (2017) Syp1 regulates the clathrin-mediated and clathrin-independent endocytosis of multiple cargo proteins through a novel sorting motif. Mol. Biol. Cell 28, 2434-48.
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Zhang, W., Sartori, M. A., Makhnevych, T., Federowicz, K. E., Dong, X., Liu, L., Nim, S., Dong, A., Yang, J., Li, Y., Haddad, D., Ernst, A., Heerding, D., Tong, Y., Moffat, J. & Sidhu, S. S. (2017) Generation and validation of intracellular ubiquitin variant inhibitors for USP7 and USP10. J. Mol. Biol. 429, 3546-60.
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Zhang, W., Bailey-Elkin, B. A., Knaap, R. C. M., Khare, B., Dalebout, T. J., Johnson, G. G., van Kasteren, P. B., McLeish, N. J., Gu, J., He, W., Kikkert, M., Mark, B. L. & Sidhu, S. S. (2017) Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants. PLoS Pathog. 13, e1006372.
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Ling, B., Watt, K., Banerjee, S., Newsted, D., Truesdell, P., Adams, J., Sidhu, S. S. & Craig, A. W. (2017) A novel immunotherapy targeting MMP-14 limits hypoxia, immune suppression and metastasis in triple-negative breast cancer models. Oncotarget 8, 58372-85.
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Gorelik, M. & Sidhu, S. S. (2017) Specific targeting of the deubiquitinase and E3 ligase families with engineered ubiquitin variants. Bioeng. Transl. Med. 2, 31-42.
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Qazi, M. A., Vora, P., Venugopal, C., Sidhu, S. S., Moffat, J., Swanton, C. & Singh, S. K. (2017) Intratumoral heterogeneity: Pathways to treatment resistance and relapse in human glioblastoma. Ann. Oncol. 28, 1448-56.
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Miersch, S., Maruthachalam, B. V., Geyer, C. R. & Sidhu, S. S. (2017) Structure-Directed and Tailored Diversity Synthetic Antibody Libraries Yield Novel Anti-EGFR Antagonists. ACS Chem. Biol. 12, 1381-9.
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Manczyk, N., Yates, B.P., Veggiani, G., Ernst, A., Sicheri, F. & Sidhu, S. S. (2017) Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif. Protein Sci. 26, 1060-9.
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Liu, H., Saxena, A., Sidhu, S. S. & Wu, D. (2017) Fc engineering for developing therapeutic bispecific antibodies and novel scaffolds. Front. Immunol. 8, 38.
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Huang, H., Kaneko, T., Sidhu, S. S., Li, S. S. (2017) Creation of phosphotyrosine superbinders by directed evolution of an SH2 domain. Methods Mol. Biol. 1555, 225-54.
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Liang, J., Sagum, C. A., Bedford, M. T., Sidhu, S. S., Sudol, M., Han, Z. & Harty, R. N. (2017) Chaperone-mediated autophagy protein BAG3 negatively regulates Ebola and Marburg VP40-Mediated Egress. PLoS Pathog. 13, e1006132.
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Leung, I., Jarvik, N. & Sidhu, S. (2017) A Highly Diverse and Functional Naïve Ubiquitin Variant Library for Generation of Intracellular Affinity Reagents. J. Mol. Biol. 429, 115-27.
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Tong, J., Cao, B., Martyn, G. D., Krieger, J. R., Taylor, P., Yates, B., Sidhu, S. S., Li, S. S. C., Mao, X. & Moran, M. F. (2017) Protein-phosphotyrosine proteome profiling by superbinder-SH2 domain affinity purification mass spectrometry, sSH2-AP-MS. Proteomics 17, issue 6.
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Steinhart, Z., Pavlovic, Z., Chandrashekhar, M., Hart, T., Wang, X., Zhang, X., Robitaille, M., Brown, K. R., Jaksani, S., Overmeer, R., Boj, S. F., Adams, J., Pan, J., Clevers, H., Sidhu, S., Moffat, J. & Angers, S. (2017) Genome-wide CRISPR screens reveal a Wnt-FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors. Nat. Med. 23, 60-8.
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Stolz, A., Putyrski, M., Kutle, I., Huber, J., Wang, C., Major, V., Sidhu, S. S., Youle, R. J., Rogov, V. V., Dötsch, V., Ernst, A. & Dikic, I. (2016) Fluorescence‐based ATG8 sensors monitor localization and function of LC3/GABARAP proteins. EMBO J. 36, 549-64.
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Nilvebrant, J., Tessier, P. M. & Sidhu, S. S. (2016) Engineered autonomous human variable domains. Curr. Pharm. Des. 22, 6527-37.
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Yamaguchi, M., VanderLinden, R., Weissmann, F., Qiao, R., Dube, P., Brown, N. G., Haselbach, D., Zhang, W., Sidhu, S. S., Peters, J. M., Stark, H. & Schulman, B. A. (2016) Cryo-EM of Mitotic Checkpoint Complex-Bound APC/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation. Mol. Cell 63, 593-607.
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Miersch, S. & Sidhu, S. S. (2016) Intracellular targeting with engineered proteins.
F1000Res 5, 1947.
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Han, Z., Sagum, C. A., Bedford, M. T., Sidhu, S. S., Sudol, M. & Harty, R. N. (2016) ITCH E3 ubiquitin ligase interacts with Ebola virus VP40 to regulate budding. J. Virol. 90, 9163-71.
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Gray, A. C., Sidhu, S. S., Chandrasekera, P. C., Hendriksen, C. F. & Borrebaeck, C. A. (2016) Animal-based antibodies: Obsolete. Science 353, 452-3.
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Gray, A. C., Sidhu, S. S., Chandrasekera, P. C., Hendriksen, C. F. & Borrebaeck, C. A. (2016) Animal-Friendly Affinity Reagents: Replacing the Needless in the Haystack. Trends Biotechnol. 34, 960-9.
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Leung, I., Dekel, A., Shifman, J. M. & Sidhu, S. S. (2016) Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21. Proc. Natl. Acad. Sci. USA 113, 8705-10.
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Banh, R., Iorio, C., Marcotte, R., Xu, Y., Cojocari, D., Rahman, A. A., Pawling, J., Zhang, W., Sinha, A., Rose, C., Isasa, M., Zhang, S., Wu, R., Virtanen, C., Hitomi, T., Habu, T., Sidhu, S., Koizumi, A., Wilkins, S., Kislinger, T., Gygi, S., Schofield, C., Dennis, J., Wouters, B. & Neel, B. (2016) PTP1B controls non-mitochondrial oxygen consumption by regulating RNF213 to promote tumour survival during hypoxia. Nat. Cell Biol. 18, 803-13.
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Hershey, D. M., Browne, P. J., Iavarone, A. T., Teyra, J., Lee, E. H., Sidhu, S. S. & Komeili, A. (2016) Magnetite Biomineralization in Magnetospirillum magneticum is Regulated by a Switch-like Behavior in the HtrA Protease MamE. J. Biol. Chem. 291, 17941-52.
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Brown, N. G., VanderLinden, R., Watson, E. R., Weissmann, F., Ordureau, A., Wu, K.-P., Zhang, W., Yu, S., Mercredi, P. Y., Harrison, J. S., Davidson, I. F., Qiao, R., Lu, Y., Dube, P., Brunner, M. R., Grace, C. R. R., Miller, D. J., Haselbach, D., Jarvis, M.A., Yamaguchi, M., Yanishevski, D., Petzold, G., Sidhu, S. S., Kuhlman, B., Kirschner, M. W., Harper, J. W., Peters, J.-M., Stark, H. & Schulman, B. A. (2016) Dual architectures regulate multiubiquitination and ubiquitin chain elongation for a RING E3. Cell 165, 1440-53.
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Gakhal, A. K., Jensen, T. J., Bozoky, Z., Roldan, A., Lukacs, G. L., Forman-Kay, J., Riordan, J. R. & Sidhu, S. S. (2016) Development and characterization of synthetic antibodies binding to the cystic fibrosis conductance regulator. MAbs. 16, 1-10.
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Gorelik, M., Orlicky, S., Sartori, M. A., Tang, X., Marcon, E., Kurinov, I., Greenblatt, J. F., Tyers, M., Moffat, J., Sicheri, F. & Sidhu, S. S. (2016) Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface. Proc. Natl. Acad. Sci. USA 113, 3527-32.
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Zhang, W., Wu, K.-P., Sartori, M. A., Kamadurai, H. B., Ordureau, A., Jiang, C., Mercredi, P. Y., Murchie, R., Hu, J., Persaud, A., Mukherjee, M., Li, N., Doye, A., Walker, J. R., Sheng, Y., Hao, Z., Li, Y., Brown, K. R., Lemichez, E., Chen, J., Tong, Y., Harper, J. W., Moffat, J., Rotin, D., Schulman, B. A. & Sidhu, S. S. (2016) System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes. Mol. Cell 62, 121-36.
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Na, H., Laver, J. D., Jeon, J., Singh, F., Ancevicius, K., Fan, Y., Cao, W. X., Nie, K., Yang, Z., Luo, H., Wang, M., Rissland, O., Westwood, J. T., Kim, P. M., Smibert, C. A., Lipshitz, H. D. & Sidhu, S. S. (2016) A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes. RNA 22, 636-55.
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Arita, Y., Allen, S., Chen, G., Zhang, W., Wang, Y., Owen, A., Dentinger, P. & Sidhu, S. (2016) Rapid isolation of peptidic inhibitors of the solute carrier family transporters OATP1B1 and OATP1B3 by cell-based phage display selections. Biochem. Biophys. Res. Commun. 473, 370-6.
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Garrido-Urbani, S., Garg, P., Ghossoub, R., Arnold, R., Lembo, F., Sundell, G. N., Kim, P. M., Lopez, M., Zimmermann, P., Sidhu, S. S. & Ivarsson, Y. (2016) Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. FEBS Lett. 590, 3-12.
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Uppalapati, M., Lee, D. J., Mandal, K., Li, H., Miranda, L. P., Lowitz, J., Kenney, J., Adams, J. J., Ault-Riche, D., Kent, S. B.H. & Sidhu, S. S. (2016) A Potent D-protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable and Longer-Circulating In Vivo. ACS Chem. Biol. 11, 1058-65.
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Uchime, O., Dai, Z., Biris, N., Lee, D., Sidhu, S. S., Li, S., Lai, J. R. & Gavathiotis, E. (2016) Synthetic antibodies inhibit Bcl-2-associated X protein (BAX) through blockade of the N-terminal activation site J. Biol. Chem. 291, 89-102.
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Kuruganti, S., Miersch, S., Deshpande, A., Speir, J. A., Harris, B. D., Schriewer, J. M., Buller, R. M., Sidhu, S. S. & Walter, M. R. (2016) Cytokine Activation by Antibody Fragments Targeted to Cytokine-Receptor Signaling Complexes. J. Biol. Chem. 291, 447-61.
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Adams, J. J., Narayanan, S., Birnbaum, M.E., Sidhu, S. S., Blevins, S. J., Gee, M. H., Sibener, L. V., Baker, B. M., Kranz, D. M. & Garcia, K. C. (2016) Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nat. Immunol. 17, 87-94.
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Hu, M.-C., Shi, M., Zhang, J., Addo, T., Cho, H. J., Barker, S. L., Ravikumar, P., Gillings, N., Bian, A., Sidhu, S. S., Kuro-o, M. & Moe, O. W. (2016) Renal Production, Uptake, and Handling of Circulating alpha-Klotho. J. Am. Soc. Nephrol. 27, 79-90.
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Hart, T., Chandrashekhar, M., Aregger, M., Steinhart, Z., Brown, K. R., MacLeod, G., Mis, M., Zimmermann, M., Fradet-Turcotte, A., Sun, S., Mero, P., Dirks, P., Sidhu, S., Roth, F. P., Rissland, O. S., Durocher, D., Angers, S. & Moffat, J. (2015) High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell 163, 1515-26.
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Mattera, R., Guardia, C. M., Sidhu, S. & Bonifacino, J. S. (2015) Bivalent Motif-Ear Interactions Mediate the Recruitment of the Accessory Protein Tepsin by the AP-4 Adaptor Complex. J. Biol. Chem. 290, 30736-49.
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Huang, H., Economopoulos, N. O., Liu, B. A., Uetrecht, A., Gu, J., Jarvik, N., Nadeem, V., Pawson, T., Moffat, J., Miersch, S. & Sidhu, S. S. (2015) Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. Protein Sci. 24, 1890-900.
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Van Deventer, J. A., Kelly, R. L., Rajan, S., Wittrup, K. D. & Sidhu, S. S. (2015) A switchable yeast display/secretion system. Protein Eng. Des. Sel. 28, 317-25. Cover feature.
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Hornsby, M., Paduch, M., Miersch, S., Sääf, A., Matsuguchi, T., Lee, B., Wypisniak, K., Doak, A., King, D., Usatyuk, S., Perry, K., Lu, V., Thomas, W., Luke, J., Goodman, J., Hoey, R. J., Lai, D., Griffin, C., Li, Z., Vizeacoumar, F. J., Dong, D., Campbell, E., Anderson, S., Zhong, N., Gräslund, S., Koide, S., Moffat, J., Sidhu, S., Kossiakoff, A. & Wells, J. (2015) A high through-put platform for recombinant antibodies to folded proteins. Mol. Cell. Proteomics 14, 2833-47.
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Zhong, N., Loppnau, P., Seitova, A., Ravichandran, M., Fenner, M., Jain, H., Bhattacharya, A., Hutchinson, A., Paduch, M., Lu, V., Olszewski, M., Kossiakoff, A. A., Dowdell, E., Koide, A., Koide, S., Huang, H., Nadeem, V., Sidhu, S. S., Greenblatt, J. F., Marcon, E., Arrowsmith, C. H., Edwards, A., M. & Gräslund, S. (2015) Optimizing production of antigens and Fabs in the context of generating recombinant antibodies to human proteins. PLoS One 10, e0120481.
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Marcon, E., Jain, H., Bhattacharya, A., Guo, H., Phanse, S., Pu, S., Byram, G., Collins, B. C., Dowdell, E., Fenner, M., Guo, X., Hutchinson, A., Kennedy, J. J., Krastins, B., Larsen, B., Lin, Z.-Y., Lopez, M. F., Loppnau, P., Miersch, S., Nguyen, T., Olsen, J. B., Paduch, M., Ravichandran, M., Seitova, A., Vadali, G., Vogelsang, M. S., Whiteaker, J. R., Zhong, G., Zhong, N., Zhao, L., Aebersold, R., Arrowsmith, C. H., Emili, A., Frappier, L., Gingras, A.-C., Gstaiger, M., Paulovich, A. G., Koide, S., Kossiakoff, A. A., Sidhu, S. S., Wodak, S. J., Gräslund, S., Greenblatt, J. F. & Edwards, A. M. (2015) Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat. Methods 12, 725-31.
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Laver, J. D., Li, X., Ray, D., Cook, K. B., Hahn, N. A., Nabeel-Shah, S., Kekis, M., Luo, H., Marsolais, A. J., Fung, K. Y., Hughes, T. R., Westwood, J. T., Sidhu, S. S., Morris, Q., Lipshitz, H. D. & Smibert, C. A. (2015) Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biol. 16, 94.
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Chen, G., Gorelik, L., Simon, K. J., Pavlenco, A., Cheung, A., Brickelmaier, M., Chen, L. L., Jin, P., Weinreb, P. H. & Sidhu, S. S. (2015) Synthetic antibodies and peptides recognizing progressive multifocal leukoencephalopathy-specific point mutations in polyomavirus JC capsid viral protein 1. MAbs. 7, 681-92.
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Luz, D., Chen, G., Maranhão, A. Q., Rocha, L. B., Sidhu, S. & Piazza, R. M. (2015) Development and characterization of recombinant antibody fragments that recognize and neutralize in vitro Stx2 Toxin from Shiga Toxin-producing Escherichia coli. PLoS One 10, e0120481.
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Fellouse, F. A. & Sidhu, S. (2015) Synthetic Antibody Libraries. In “Phage display in drug discovery and Biotechnology, Second Edition” (S. S. Sidhu & C. R. Geyer, Eds.), Chapter 18, pp 495-520, CRC Press, Boca Raton, FL.
Tomic, J., McLaughlin, M., Hart, T., Sidhu, S. & Moffat, J. (2015) Leveraging Synthetic Phage-Antibody Libraries for Panning on the Mammalian Cell Surface. In “Phage display in drug discovery and Biotechnology, Second Edition” (S. S. Sidhu & C. R. Geyer, Eds.), Chapter 5, pp 113-22, CRC Press, Boca Raton, FL.
Miersch, S., Li, Z., Hanna, R., McLaughlin, M. E., Hornsby, M., Matsuguchi, T., Paduch, M., Sääf, A., Wells, J., Koide, S., Kossiakoff, A. & Sidhu, S. S. (2015) Scalable high throughput selection from phage-displayed synthetic antibody libraries. J. Vis. Exp. 95, Immunology and Infection, January 17 [video 51492].
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Boyle, A. J., Cao, P. J., Hedley, D. W., Sidhu, S. S., Winnik, M. A. & Reilly, R. M. (2015) MicroPET/CT imaging of patient-derived pancreatic cancer xenografts implanted subcutaneously or orthotopically in NOD-scid mice using 64Cu-NOTA-panitumumab F(ab')2 fragments. Nucl. Med. Biol. 42, 71-7.
Abstract on PubMed
Barker, S. L., Pastor, J., Carranza, D., Quiñones, H., Griffith, C., Goetz, R., Mohammadi, M., Ye, J., Zhang, J., Hu, M. C., Kuro-O, M., Moe, O. W. & Sidhu, S. S. (2015) The demonstration of αKlotho deficiency in human chronic kidney disease with a novel synthetic antibody. Nephrol. Dial. Transplant. 30, 223-33.
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Ren, L., Willet, A. H., Roberts-Galbraith, R. H., McDonald, N. A., Feoktistova, A., Chen, J. S., Huang, H., Guillen, R., Boone, C., Sidhu, S. S., Beckley, J. R. & Gould, K. L. (2015) The Cdc15 and Imp2 SH3 domains cooperatively scaffold a network of proteins that redundantly ensure efficient cell division in fission yeast. Mol. Biol. Cell 26, 256-69.
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Jeon, J., Nim, S., Teyra, J., Datti, A., Wrana, J. L., Sidhu,
S. S., Moffat, J. & Kim, P. M. (2014) A systematic
approach to identify novel cancer drug targets using machine
learning, inhibitor design and high-throughput screening. Genome
Med. 6, 57.
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Ernst, A., Appleton, B. A., Ivarsson, Y., Zhang, Y., Gfeller,
D., Wiesmann, C & Sidhu, S. S. (2014) A structural
portrait of the PDZ domain family. J. Mol. Biol. 426, 3509-19.
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Chen, G., Koellhoffer, J. F., Zak, S. E., Frei, J. C., Liu, N.,
Long, H., Yi, W., Nagar, K., Pan, G., Chandran, K., Dye, J. M.,
Sidhu, S. S. & Lai, J. R. (2014) Synthetic Antibodies
with a Human Framework that Protect Mice from Lethal Sudan
Ebolavirus Challenge. ACS Chem. Biol. 9, 2263-73.
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Shukla, A. K., Westfield, G. H., Xiao, K., Reis, R. I., Huang,
L. Y., Tripathi-Shukla, P., Qian, J., Li, S., Blanc, A.,
Oleskie, A. N., Dosey, A. M., Su, M., Liang, C. R., Gu, L. L.,
Shan, J. M., Chen, X., Hanna, R., Choi, M., Yao, X. J., Klink,
B. U., Kahsai, A. W., Sidhu, S. S., Koide, S., Penczek,
P. A., Kossiakoff, A. A., Woods Jr, V. L., Kobilka, B. K.,
Skiniotis, G. & Lefkowitz, R. J. (2014) Visualization of
arrestin recruitment by a G-protein-coupled receptor. Nature
512, 218-22.
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Ni, Z., Xu, C., Guo, X., Hunter, G. O., Kuznetsova, O. V.,
Tempel, W., Marcon, E., Zhong, G., Guo, H., Kuo, W. H., Li, J.,
Young, P., Olsen, J. B., Wan, C., Loppnau, P., El Bakkouri, M.,
Senisterra, G. A., He, H., Huang, H., Sidhu, S. S.,
Emil, A., Murphy, S., Mosley, A. L., Arrowsmith, C. H., Min, J.
& Greenblatt, J. F. (2014) RPRD1A and RPRD1B are human RNA
polymerase II C-terminal domain scaffolds for Ser5
dephosphorylation. Nat. Struct. Mol. Biol. 21, 686-95.
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Murciano-Calles, J., McLaughlin, M. E., Erijman, A., Hooda, Y.,
Chakravorty, N., Martinez, J. C., Shifman, J. M., Sidhu, S.
S. (2014) Alteration of the C-terminal ligand specificity
of the Erbin PDZ domain by allosteric mutational effects. J.
Mol. Biol. 426, 3500-8.
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Gfeller, D., Ernst, A., Jarvik, N., Sidhu, S. S. &
Bader, G. D. (2014) Prediction and experimental characterization
of nsSNPs altering human PDZ-binding motifs. PLoS One 9, e94507.
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Adams, J. J. & Sidhu, S. S. (2014) Synthetic
antibody technologies. Curr. Opin. Struct. Biol. 24C, 1-9.
Abstract
on PubMed
Abu-Odeh, M., Bar-Mag, T., Huang, H., Kim, T., Salah, Z.,
Abdeen, S. K., Sudol, M., Reichmann, D., Sidhu, S. S.,
Kim, P. M. & Aqeilan, R. I. (2014) Characterizing WW Domain
Interactions of Tumor Suppressor WWOX Reveals its Association
with Multiprotein Networks. J. Biol. Chem. 28, 8865-80.
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Ivarsson, Y., Arnold, R., McLaughlin, M., Nim, S., Joshi, R.,
Ray, D., Liu, B., Teyra, J., Pawson, T., Moffat, J., Li, S.-S.,
Sidhu, S. S. & Kim, P. M. (2014) Large-scale
interaction profiling of PDZ domains through proteomic
peptide-phage display using human and viral phage peptidomes.
Proc. Natl. Acad. Sci. USA 111, 2542-7.
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Chen, G. & Sidhu, S. S. (2014) Design and
generation of synthetic antibody libraries for phage display.
Methods Mol. Biol. 1131, 113-31.
Abstract
on PubMed
Liu, P., Cai, Z., Kang, J. W., Boyle, A. J., Adams, J., Lu, Y.,
Mbong, G. N., Sidhu, S. S., Reilly, R. M. & Winnik,
M. A. (2014) Intracellular Routing in Breast Cancer Cells of
Streptavidin-Conjugated Trastuzumab Fab Fragments Linked to
Biotinylated Doxorubicin-Functionalized Metal Chelating
Polymers. Biomacromolecules 15, 715-25.
Abstract
on PubMed
Yu, C. G., Tonikian. R., Felsensteiner, C., Jhingree, J. R.,
Desveaux, D., Sidhu, S. S. & Harris, T. J. (2014)
Peptide binding properties of the three PDZ domains of bazooka
(Drosophila par-3). PLoS One 9, e86412.
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Huang, H., Ceccarelli, D. F., Orlicky, S., St-Cyr, D. J.,
Ziemba, A., Garg, P., Plamondon, S., Auer, M., Sidhu, S. S.,
Marinier, A., Kleiger, G., Tyers, M. & Sicheri, F. (2014) E2
enzyme inhibition by stabilization of a low-affinity interface
with ubiquitin. Nat. Chem. Biol. 10, 156-63.
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Zhang, W. & Sidhu, S. S. (2014) Development of
inhibitors in the ubiquitin cascade. FEBS Lett. 588, 356-67.
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Adams, J. J., Nelson, B. & Sidhu, S. S. (2014)
Recombinant genetic libraries and human monoclonal antibodies.
Methods Mol. Biol. 1060, 149-70.
Abstract
on PubMed
Reshetnyak, A. V., Nelson, B., Shi, X., Boggon, T.J., Pavlenco,
A., Mandel-Bausch, E. M., Tome, F., Suzuki, Y., Sidhu, S. S.,
Lax, I. & Schlessinger, J. (2013) Structural basis for KIT
receptor tyrosine kinase inhibition by antibodies targeting the
D4 membrane-proximal region. Proc. Natl. Acad. Sci. USA 110,
17832-7.
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Owen, S. C., Patel, N., Logie, J., Pan, G., Persson, H.,
Moffat, J., Sidhu, S. S. & Shoichet, M. S. (2013)
Targeting HER2+ breast cancer cells: Lysosomal accumulation of
anti-HER2 antibodies is influenced by antibody binding site and
conjugation to polymeric nanoparticles. J. Control. Release.
172, 395-404.
Abstract
on PubMed
Ernst, A. & Sidhu, S. S. (2013) Engineering
ubiquitin to modulate the ubiquitin proteasome system. Cell
Cycle 12, 1651-2.
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Hu, M.-C., Shi, M., Cho, H. J., Zhang, J., Pavlenco, A., Sidhu, S. S., Huang, L. J.-S. & Moe, O. W. (2013) The
erythropoietin receptor is a downstream effector of
Klotho-induced cytoprotection. Kidney Int. 84, 468-81.
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Xin, X., Gfeller, D., Cheng, J., Tonikian, R, Sun, L., Guo, A.,
Lopez, L., Pavlenco, A., Akintobi, A., Zhang, Y., Rual, J. F.,
Currell, B., Seshagiri, S., Hao, T., Yang, X., Shen, Y. A.,
Salehi-Ashtiani, K., Li, J., Cheng, A. T., Bouamalay, D.,
Lugari, A., Hill, D. E., Grimes, M. L, Drubin, D. G., Grant, B.
D., Vidal, M., Boone, C., Sidhu, S. S. & Bader, G.
D. (2013) SH3 interactome conserves general function over
specific form. Mol. Syst. Biol. 9, 652.
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Ma, X., Barthelemy, P. A., Rouge, L., Wiesmann, C. & Sidhu, S. S. (2013) Design of Synthetic Autonomous VH Domain
Libraries and Structural Analysis of a VH Domain Bound to
Vascular Endothelial Growth Factor. J. Mol. Biol. 425, 2247-59.
Abstract
on PubMed
Findlay, G. M., Smith, M. J., Lanner, F., Hsiung, M. S., Gish,
G. D., Petsalaki, E., Cockburn, K., Kaneko, T., Huang, H,
Bagshaw, R. D., Ketela, T., Tucholska, M., Taylor, L., Botwell,
D. D., Moffat, J., Ikura, M., Li, S. S., Sidhu, S. S.,
Rossant, J. & Pawson, T. (2013) Interaction domains of
Sos1/Grb2 are finely tuned for cooperative control of embryonic
stem cell fate. Cell 152, 1008-20.
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McLaughlin, M. E. & Sidhu, S. S. (2013) Engineering
and analysis of peptide-recognition domain specificities by
phage display and deep sequencing. Methods Enzymol. 523, 327-49.
Abstract
on PubMed
Ernst, A., Avvakumov, G., Tong, J., Fan, Y., Zhao, Y., Alberts,
P., Persaud, A., Walker, J. R., Neculai, A. M., Neculai, D.,
Vorobyov, A., Garg, P., Beatty, L., Chan, P. K., Juang, Y. C.,
Landry, M. C., Yeh, C., Zeqiraj, E., Karamboulas, K.,
Allali-Hassani, A., Vedadi, M., Tyers, M., Moffat, J., Sicheri,
F., Pelletier, L., Durocher, D., Raught, B., Rotin, D., Yang,
J., Moran, M. F., Dhe-Paganon S. & Sidhu, S. S.
(2013) A Strategy for Modulation of Enzymes in the Ubiquitin
System. Science 339, 590-5.
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Rojas, G., Pupo, A., Leon, K., Avellanet, J., Carmenate, T.
& Sidhu, S. (2013) Deciphering the molecular bases of the
biological effects of antibodies against Interleukin-2: a
versatile platform for fine epitope mapping. Immunobiology 218,
105-13.
Abstract
on PubMed
Persson, H., Ye, W., Wernimont, A., Adams, J. J., Lam, R. &
Sidhu, S. S. (2012) CDR-H3 Diversity is Not Required For
Antigen Recognition by Synthetic Antibodies. J. Mol. Biol. 425,
803-11.
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Ahmed, S. M., Thériault, B. L., Uppalapati, M., Chiu, C. W.,
Gallie, B. L., Sidhu, S. S. & Angers, S. (2012)
KIF14 negatively regulates Rap1a-Radil signaling during breast
cancer progression. J. Cell Biol. 199, 951-67.
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Miersch, S. & Sidhu, S. S. (2012) Immunology:
Evolving superkines for selectivity. Nat. Chem. Biol. 8, 955-6.
Abstract
on PubMed
Koellhoffer, J. F., Chen, G., Sandesara, R. G., Bale, S.
Saphire, E. O., Chandran, K., Sidhu, S. S. & Lai, J.
R. (2012) Two synthetic antibodies that recognize and neutralize
distinct proteolytic forms of the Ebola virus envelope
glycoprotein. Chembiochem. 13, 2549-57.
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Orava, E. W., Jarvik, N., Shek, Y. L., Sidhu, S. S.
& Gariepy, J. (2013) A short DNA Aptamer that Recognizes
TNFα and blocks its activity in vitro. ACS Chem. Biol. 8, 170-8.
Abstract
on PubMed
Kaneko, T., Huang, H., Cao, X., Li, X., Li, C., Voss, C., Sidhu, S. S. & Li, S. S. (2012) Superbinder SH2 domains act
as antagonists of cell signaling. Sci. Signal. 5, ra68.
Abstract
on PubMed
Mandal, K., Uppalapati, M., Ault-Riche, D., Kenney, J., Lowitz,
J., Sidhu, S. S., Kent, S. B. (2012) Chemical synthesis
and X-ray structure of a heterochiral {D-protein antagonist plus
vascular endothelial growth factor} protein complex by racemic
crystallography. Proc. Natl. Acad. Sci. USA 109, 14779-84.
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Miller, K. R, Koide, A., Leung, B., Fitzsimmons, J., Yoder, B.,
Yuan, H., Jay, M., Sidhu, S. S., Koide, S. &
Collins, E. J. (2012) T cell receptor-like recognition of tumor
in vivo by synthetic antibody fragment. PLoS One 7, e43746.
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Tonikian, R. & Sidhu, S. S. (2012) Selecting and
purifying autonomous human variable heavy (VH) domains. Methods
Mol. Biol. 911, 327-53.
Abstract
on PubMed
Zalatan, J. G, Coyle, S. M., Rajan, S., Sidhu, S. S.
& Lim, W. A. (2012) Conformational control of the Ste5
scaffold protein insulates against MAP kinase misactivation.
Science 337, 1218-22.
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Miersch, S. & Sidhu, S. S. (2012) Synthetic
antibodies: concepts, potential and practical considerations.
Methods 57, 486-98.
Abstract
on PubMed
Nelson, B. & Sidhu, S. S. (2012) Synthetic antibody
libraries. Methods Mol. Biol. 899, 27-41.
Abstract
on PubMed
Geyer, C. R., McCafferty, J., Dübel, S., Bradbury, A. R. &
Sidhu, S. S. (2012) Recombinant antibodies and in vitro
selection technologies. Methods Mol. Biol. 901, 11-32.
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Teyra, J., Sidhu, S. S. & Kim, P. M. (2012)
Elucidation of the binding preferences of peptide recognition
modules: SH3 and PDZ domains. FEBS Lett. 586, 2613-7.
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Sidhu, S. S. (2012) Antibodies for All: The Case for
Genome-wide Affinity Reagents. FEBS Lett. 586, 2778-9.
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Karauzum, H.*, Chen, G.*, Abaandou, L., Mahmoudieh, M., Boroun,
A. R., Shulenin, S., Devi, V. S., Stavale, E., Warfield, K. L.,
Zeitlin, L., Roy, C. J., Sidhu, S. S. & Aman, M. J.
(2012) Synthetic human monoclonal antibodies towards
staphylococcal enterotoxin B (SEB) protective against toxic
shock syndrome. J. Biol. Chem. 287, 25203-15. * equal
contribution
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Laver, J. D., Ancevicius, K., Sollazzo, P., Westwood, J. T., Sidhu, S. S., Lipshitz, H. D. & Smibert, C. A. (2012)
Synthetic antibodies as tools to probe RNA-binding protein
function. Molec. Biosyst. 8, 1650-7.
Abstract
on PubMed
Kim, T., Tyndel, M. S., Huang, H., Sidhu, S. S., Bader,
G. D., Gfeller, D. & Kim, P. M. (2012) MUSI: an integrated
system for identifying multiple specificity from very large
peptide or nucleic acid data sets. Nucl. Acids Res. 40, e47.
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McCluskey, A. J., Bolewska-Pedyczak, E., Jarvik, N., Chen, G.,
Sidhu, S. S. & Gariépy, J. (2012) Charged and
hydrophobic surfaces on the a chain of shiga-like toxin 1
recognize the C-terminal domain of ribosomal stalk proteins.
PLoS One 7, e31191.
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Rajan, S. & Sidhu, S. S. (2012) Simplified
synthetic antibody libraries. Methods Enzymol. 502: 3-23.
Abstract
on PubMed
Huang, H. & Sidhu, S. S. (2011) Studying binding
specificities of peptide recognition modules by high-throughput
phage display selections. Methods Mol. Biol. 781, 87-97.
Abstract
on PubMed
Yip, K. Y., Utz, L., Sitwell, S., Hu, X., Sidhu, S. S.,
Turk, B. E., Gerstein, M. B. & Kim, P. M. (2011)
Identification of specificity determining residues in peptide
recognition domains using an information theoretic approach
applied to large-scale binding maps. BMC Biol. 9, 53.
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Bahudhanapati, H., Zhang, Y., Sidhu, S. S. & Brew,
K. (2011) Phage display of tissue inhibitor of
metalloproteinases-2 (TIMP-2): Identification of selective
inhibitors of collagenase-1 (MMP-1). J. Biol. Chem. 286,
31761-70.
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Colwill, K.; Renewable Protein Binder Working Group; In vitro
Antibody Consortium, Persson, H., Jarvik, N. E., Wyrzucki, A.,
Wojcik, J., Koide, A., Kossiakoff, A. A., Koide, S., Sidhu,
S. S., Dyson, M. R., Pershad, K., Pavlovic, J. D.,
Karatt-Vellatt, A., Schofield, D. J., Kay, B. K., McCafferty,
J., Mersmann, M., Meier, D., Mersmann, J., Helmsing, S., Hust,
M., Dübel, S.; Monash Antibody Technologies Facility, Berkowicz,
S., Freemantle, A., Spiegel, M., Sawyer, A., Layton, D., Nice,
E.; Pawson Laboratory, Dai, A., Rocks, O., Williton, K.,
Fellouse, F. A., Hersi, K., Pawson, T.; Human Protein Atlas,
Nilsson, P., Sundberg, M., Sjöberg, R., Sivertsson, A., Schwenk,
J. M., Takanen, J. O., Hober, S., Uhlén, M.; Structural Genomics
Consortium, Dahlgren, L. G., Flores, A., Johansson, I., Weigelt,
J., Crombet, L., Loppnau, P., Kozieradzki, I., Cossar, D.,
Arrowsmith, C. H., Edwards, A. M. & Gräslund, S. (2011) A
roadmap to generate renewable protein binders to the human
proteome. Nat. Methods 8, 551-8.
Abstract
on PubMed
Gfeller, D., Butty, F., Wierzbicka, M., Verschueren, E.,
Vanhee, P., Huang, H., Ernst, A., Dar, N., Stagljar, I.,
Serrano, L., Sidhu, S. S., Bader, G. D. & Kim, P. M.
(2011) The multiple-specificity landscape of modular peptide
recognition domains. Mol. Syst. Biol. 7, 484.
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Qazi, O., Rani, M., Gnanam, A. J., Cullen, T. W., Stead, C. M.,
Kensing, H., McCaul, K., Ngugi, S., Prior, J. L., Lipka, A.,
Nagy, J. M., Gregory, C. W., Judy, B. M., Harding, S. V.,
Titball, R. W., Sidhu, S. S., Trent, M. S., Kitto, G.
B., Torres, A., Estes, D. M., Iverson, B., Georgiou, G. &
Brown, K. A. (2011) Development of reagents and assays for the
detection of pathogenic Burkholderia species. Faraday Discuss.
149, 23-36.
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Bradbury, A. R., Sidhu, S. S., Dübel, S., &
McCafferty, J. (2011) Beyond natural antibodies: the power of in
vitro display technologies. Nat. Biotechnol. 29, 245-54.
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Kaneko, T., Sidhu, S. S. & Li, S. S. (2011)
Evolving specificity from variability for protein interaction
domains. Trends Biochem. Sci. 36, 183-90.
Abstract
on PubMed
Koldobskaya, Y., Duguid, E. M., Shechner, D. M., Suslov, N. B.,
Ye, J., Sidhu, S. S., Bartel, D. P., Koide, S.,
Kossiakoff, A. A. & Piccirilli, J. A. (2011) A portable RNA
sequence whose recognition by a synthetic antibody facilitates
structural determination. Nat. Struct. Mol. Biol. 18, 100-6.
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Oka, T., Remue, E., Meerschaert, K., Vanloo, B., Boucherie,
C., Gfeller, D., Bader, G. D., Sidhu, S. S.,
Vandekerckhove, J., Gettemans, J. & Sudol, M. (2010)
Functional complex between YAP2 and ZO-2 is PDZ domain
dependent, regulates YAP2 nuclear localization and signaling.
Biochem. J. 432, 461-72.
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Ernst, A., Gfeller, D., Kan, Z., Seshagiri, S., Kim, P. M.,
Bader, G.D. & Sidhu, S. S. (2010) Coevolution of PDZ
domain-ligand interactions analyzed by high-throughput phage
display and deep sequencing. Mol. Biosyst. 6, 1782-90.
Abstract
on PubMed
Fisher, R. D., Ultsch, M., Lingel, A., Schaefer, G., Shao, L.,
Birtalan, S., Sidhu, S. S. & Eigenbrot, C. (2010)
Structure of the complex between HER2 and an antibody paratope
formed by side chains from tryptophan and serine. J. Mol. Biol.
402, 217-29.
Abstract
on PubMed
Lam, H. Y. K., Kim, P. M., Mok, J., Tonikian, R., Sidhu, S.
S., Turk, B. E., Snyder, M. & Gerstein, M. B. (2010)
MOTIPS: Automated motif analysis for predicting targets of
modular protein domains. BMC Bioinformatics. 11, 243.
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Birtalan, S., Fisher, R. D. & Sidhu, S. S. (2010)
The functional capacity of the natural amino acids for molecular
recognition. Mol. Biosyst. 6, 1186-94.
Abstract
on PubMed
Pal, G. & Sidhu, S. S. (2009) Mapping protein function by combinatorial mutagenesis. In “Computational protein-protein interactions” (R. Nussinov & G. Schreiber, Eds.), pp 57-86, CRC Press, Boca Raton, FL.
Ernst, A. & Sidhu, S. S. (2009) Phage Display. In “Protein Engineering and Design” (S. Park and J. Cochran, Eds), pp1-22, Taylor and Francis: Boca Raton.
Li, B., Xi, H., Diehl, L., Lee, W. P., Sturgeon, L., Chinn, J.,
DeForge, L., Kelley, R. F., Wiesmann, C., van Lookeren Campagne,
M. & Sidhu, S. S. (2009) Improving therapeutic
efficacy of a complement receptor by structure-based affinity
maturation. J. Biol. Chem. 284, 35605-11.
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Tonikian, R., Xin, X., Toret, C. P., Gfeller, D., Landgraf, C.,
Panni, S., Paoluzi, S., Castagnoli, L, Currell, B., Seshagiri,
S., Yu, H. Winsor, B., Vidal, M., Davidson, A. R., Gerstein, M.
B., Bader, G. D., Volkmer, R., Cesarini, G., Drubin, D. G., Kim,
P. M., Sidhu, S. S. & Boone, C. (2009) Bayesian
modeling of the yeast SH3 domain interactome predicts
spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 7,
e1000218.
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Ernst, A., Sazinsky, S. L., Hui, S., Currell, B., Dharsee, M.,
Seshagiri, S., Bader, G. D. & Sidhu, S. S. (2009)
Rapid evolution of functional complexity in a domain family.
Sci. Signal. 2, ra50.
Abstract
on PubMed
Uysal, S., Vasquez, V., Esaiki, K., Fellouse, F. A., Sidhu,
S. S., Koide, S., Perozo, E. & Kossiakoff, A. A.
(2009) Crystal structure of full-length KcsA in its closed
conformation. Proc. Natl. Acad. Sci. USA 106, 6644-9.
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Koide, S. & Sidhu, S. S. (2009) The importance of
being tyrosine: Lessons in molecular recognition from minimalist
synthetic binding proteins. ACS Chem. Biol. 4, 325-34.
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Zhang, Y., Appleton, B. A., Wiesmann, C., Lau, T., Costa, M.,
Hannoush, R. N. & Sidhu, S. S. (2009) Inhibition of
Wnt/b-catenin signaling by peptides that target dishevelled PDZ
domains. Nat. Chem. Biol. 5, 217-9.
Abstract
on PubMed
Gao, J., Sidhu, S. S. & Wells, J. A. (2009)
Two-state selection of conformation-specific antibodies. Proc.
Natl. Acad. Sci. USA 106, 3071-6.
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Tonikian, R., Zhang, Y., Sazinsky, S. L., Currell, B., Yeh, J.
-H., Reva, B., Held, H. A., Appleton, B. A., Evangelista, M.,
Wu, Y., Xin, X., Chan, A. C., Seshagiri, S., Sander, C., Lasky,
L. A., Boone, C., Bader, G. D. & Sidhu, S. S. (2008)
A specificity map for the PDZ domain family. PLoS Biol. 6, e239.
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Newton, K., Matsumoto, M. L., Wertz, I. E., Kirkpatrick, D. S.,
Lill, J. R., Tan, J., Dugger, D., Gordon, N., Sidhu, S. S.,
Fellouse, F. A., Komuves, L., French, D. M., Ferrando, R. E.,
Lam, C., Compaan, D., Yu, C., Bosanac, I., Hymowitz, S. G.,
Kelly, R. F. & Dixit, V. M. (2008) Ubiquitin chain editing
revealed by polyubiquitin linkage-specific antibodies. Cell 134,
668-78.
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Gilbreth, R. N, Esaki, K., Koide, A., Sidhu, S. S.
& Koide, S. (2008) A dominant conformational role for amino
acid diversity in minimalist protein-protein interfaces. J. Mol.
Biol. 381, 407-18.
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Michnick, S. W. & Sidhu, S. S. (2008) Submitting
antibodies to binding arbitration. Nat. Chem. Biol. 4, 326-9.
Abstract
on PubMed
Yeh, J.-H., Sidhu, S. S. & Chan, A. C. (2008)
Regulation of a late phase of T cell polarity and effector
functions by Crtam. Cell 132, 846-59.
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Birtalan, S., Zhang, Y., Fellouse, F. A., Shao, L., Schaefer,
G. & Sidhu, S. S. (2008) The intrinsic contributions
of tyrosine, serine, glycine and arginine to the affinity and
specificity of antibodies. J. Mol. Biol. 337, 1518-28.
Abstract
on PubMed
Barthelemy, P. A., Raab, H., Appleton, B. A., Bond, C. J., Wu,
P., Wiesmann, C. & Sidhu, S. S. (2008) Comprehensive
analysis of the factors contributing to the stability and
solubility of autonomous human VH domains. J. Biol. Chem. 138,
3639-54.
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Ye, J.-D., Tereshko, V., Frederiksen, J. K., Koide, A.,
Fellouse, F. A., Sidhu, S. S., Koide, S., Kossiakoff, A.
A. & Piccirilli, J. A. (2007) Antibodies that bind RNA:
selection and co-crystallization. Proc. Natl. Acad. Sci. USA.
105, 82-7.
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Alto, N. M., Weflen, A. W., Rardin, M. J., Yarar, D., Lazar, C.
S., Tonikian, R., Koller, A., Taylor, S. S., Boone, C., Sidhu, S. S., Schmid, S. L., Hecht, G. A. & Dixon, J. E.
(2007) The type III effector EspF coordinates membrane
trafficking by the spatiotemporal activation of two eukaryotic
signaling pathways. J. Cell Biol. 178, 1265-78.
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Sidhu, S. S. & Koide, S. (2007) Phage display for
engineering and analyzing protein interaction interfaces. Curr.
Opin. Struct. Biol. 17, 481-7.
Abstract
on PubMed
Fellouse, F. A., Esaki, K., Birtalan, S., Raptis, J.,
Cancasci, V. J., Koide, A., Jhurani, P., Vasser, M., Wiesmann,
C., Kossiakoff, A. A., Koide, S. & Sidhu, S. S.
(2007) High-throughput generation of synthetic antibodies from
highly functional minimalist phage-displayed libraries. J. Mol.
Biol. 373, 924-40.
Abstract
on PubMed
Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu,
P., Pan, B., Wiesmann, C., Skelton, N. J. & Sidhu, S. S.
(2007) Structural and functional analysis of the PDZ domains of
human HtrA1 and HtrA3. Protein Sci. 16, 2454-71.
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Zhang, Y., Appleton, B. A., Wu, P., Wiesmann, C. & Sidhu, S. S. (2007) Structural and functional analysis of the
ligand specificity of the HtrA2/Omi PDZ domain. Protein Sci. 16,
1738-50.
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Tonikian, R., Zhang, Y., Boone, C. & Sidhu, S. S.
(2007) Identifying specificity profiles for peptide binding
modules with phage-displayed peptide libraries. Nat. Protoc. 2,
1368-86.
Abstract
on PubMed
Gupta, R., Kus, B., Fladd, C., Wasmuth, J., Tonikian, R., Sidhu, S. S., Krogan, N. J., Parkinson, J. & Rotin, D. (2007)
Ubiquitination screen using protein microarrays for
comprehensive identification of Rsp5 substrates in yeast. Mol.
Syst. Biol. 3, 116.
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Sidhu, S. S. & Kossiakoff, A. A. (2007) Exploring
and designing protein function with restricted diversity. Curr.
Opin. Chem. Biol. 11, 347-54.
Abstract
on PubMed
Sidhu, S. S. (2007)
Full-length antibodies on display. Nat. Biotechnol. 25, 537-8.
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Fellouse, F. A. & Sidhu, S. S. (2007) Making antibodies in bacteria. In “Making and using antibodies” (G. C. Howard & M. R. Kaser, Eds.), pp157-180, CRC Press, Boca Raton, FL.
Sidhu, S. S., Feld, B. K. & Weiss, G. A. (2007)
M13 bacteriophage coat proteins engineered for improved phage display. Methods Mol. Biol. 352, 205-19.
Abstract
on PubMed
Sidhu, S. S. & Fellouse, F. A. (2006) Synthetic
therapeutic antibodies. Nat. Chem. Biol. 12, 682-8.
Abstract
on PubMed
Li, B., Totpal, K., Russell, S., Yeh, S., Wong, W. L.,
Cochran, A., Ashkenazi, A., Hymowitz, S & Sidhu, S. S.
(2006) Activation of the proapoptotic death receptor DR5 by
oligomeric peptide and antibody agonists. J. Mol. Biol. 361,
522-36.
Abstract
on PubMed
Pal, G., Kouadio, J. -L., Artis, D. R., Kossiakoff, A. A. &
Sidhu, S. S. (2006) Comprehensive and quantitative
mapping of energy landscapes for protein-protein interactions by
rapid combinatorial scanning. J. Biol. Chem. 281, 22378-85. JBC
paper of the week. Cover feature in ASBMB Today (October, 2006).
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Appleton, B. A., Zhang, Y., Wu, P., Yin, J. P., Hunziker, W.,
Skelton, N. J. Sidhu, S. S. & Wiesmann, C. (2006)
Comparative structural analysis of the Erbin PDZ domain and the
first PDZ domain of ZO-1: Insights into determinants of PDZ
domain specificity. J. Biol. Chem. 281, 22312-20.
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Zhang, Y., Yeh, S., Appleton, B. A., Held, H. A., Kausalya, J.
P., Phua , D. C. Y., Wong, W. L., Lasky, L. A., Wiesmann, C.,
Hunziker, W. & Sidhu, S. S. (2006) Convergent and
divergent ligand specificity amongst the PDZ domains of the LAP
and zonula occludens (ZO) families. J. Biol. Chem. 281,
22299-311.
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Fellouse, F. A., Barthelemy, P. A., Kelley, R. F. & Sidhu, S. S. (2006) Tyrosine plays a dominant functional role in
the paratope of a synthetic antibody derived from a four amino
acid code. J. Mol. Biol. 357, 100-14.
Abstract
on PubMed
Fellouse, F. A. & Sidhu, S. S. (2006) Synthetic antibody libraries. In “Phage display in drug discovery and Biotechnology” (S. S. Sidhu, Ed.), pp 709-740, CRC Press, Boca Raton, FL.
Pal, G., Fong, S.-Y., Kossiakoff, A. A. & Sidhu, S. S.
(2005) Alternative views of functional protein binding epitopes
obtained by combinatorial shotgun scanning mutagenesis. Protein
Sci. 14, 2405-13.
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Fellouse, F. A., Li, B., Compaan, D. M., Peden, A. A.,
Hymowitz, S. G. & Sidhu, S. S. (2005) Molecular
recognition by a binary code. J. Mol. Biol. 348, 1153-62. Cover
feature.
Abstract
on PubMed
Bond, C., Wiesmann, C., Marsters, J. C. & Sidhu, S. S.
(2005) A structure-based database of antibody variable domain
diversity. J. Mol. Biol. 348, 699-709.
Abstract
on PubMed
Pal, G., Ultsch, M. H., Clark, P. C., Currell, B., Kossiakoff,
A. A. & Sidhu, S. S. (2005) Intramolecular
cooperativity in a protein binding site assessed by
combinatorial shotgun scanning mutagenesis. J. Mol. Biol. 347,
489-94.
Abstract
on PubMed
Lasky, L. A., Skelton, N. J. & Sidhu, S. S. (2005) PDZ domains: Intracellular mediators of carboxy-terminal protein recognition and scaffolding. In “Modular protein domains” (G. Cesarini, M. Gimona, M. Sudol & M. Yaffe, Eds.), pp 257-278, Wiley-VCH Inc., Germany.
Fellouse, F. A., Wiesmann, C. & Sidhu, S. S.
(2004) Synthetic antibodies from a four amino acid code: A
dominant role for tyrosine in antigen recognition. Proc. Natl.
Acad. Sci. USA 101, 12467-72.
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Lee, C. V., Liang, W.-C., Dennis, M. S., Eigenbrot, C., Sidhu, S. S. & Fuh, G. (2004) High affinity human antibodies
from phage-displayed synthetic Fab libraries with a single
framework scaffold. J. Mol. Biol. 340, 1073-93.
Abstract
on PubMed
Skelton, N. J., Schaffer, M. L., Deshayes, K., Blandl, T.,
Runyon, S., Nakamura, G. & Sidhu, S. S. (2004) Phage
display-derived peptide-binding provides structural insight into
insulin-like growth factor I function. Spectroscopy 18, 237-49.
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Held, H. A. & Sidhu, S. S. (2004) Comprehensive
mutational analysis of the M13 major coat protein: Improved
scaffolds for C-terminal phage display. J. Mol. Biol. 340,
587-97.
Abstract
on PubMed
Sidhu, S. S., Li, B., Chen, Y., Fellouse, F. A.,
Eigenbrot, C. & Fuh, G. (2004) Phage-displayed antibody
libraries of synthetic heavy chain complementarity determining
regions. J. Mol. Biol. 338, 299-310.
Abstract
on PubMed
Lee, C. V., Sidhu, S. S. & Fuh, G. (2004) Bivalent
antibody phage display mimics natural immunoglobulins. J.
Immunol. Methods 284, 119-32.
Abstract
on PubMed
Mattera, R., Ritter, B., Sidhu, S. S., McPherson, P. S.
& Bonifacino, J. S. (2004) Definition of the consensus motif
recognized by gamma-adaptin ear domains. J. Biol. Chem. 279,
8018-28.
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Weiss, G. A., Roth, T. A., Baldi, P. F. & Sidhu, S. S.
(2003) Comprehensive mutagenesis of the C-terminal domain of the
M13 gene-3 minor coat protein: The requirements for assembly
into the bacteriophage particle. J. Mol. Biol. 332, 777-82.
Abstract
on PubMed
Schaffer, M. L., Deshayes, K., Nakamura, G. R., Sidhu, S.
S. & Skelton, N. J. (2003) Complex with a phage
display-derived peptide provides insight into the function of
insulin-like growth factor I. Biochemistry 42, 9324-34.
Abstract
on PubMed
Bond, C., Marsters, J. C. Jr. & Sidhu, S. S. (2003)
Contributions of CDR3 to VHH domain stability and the design of
monobody scaffolds for naïve antibody libraries. J. Mol. Biol.
332, 643-55.
Abstract
on PubMed
Pal, G., Kossiakoff, A. A., Sidhu, S. S. (2003) The
functional binding epitope of a high affinity variant of human
growth hormone mapped by shotgun alanine-scanning mutagenesis:
Insights into the mechanisms responsible for improved affinity.
J. Mol. Biol. 332, 195-204.
Abstract
on PubMed
Sidhu, S. S. & Weiss, G. A. (2003) Constructing phage display libraries by oligonucleotide-directed mutagenesis. In “Phage display: A practical approach” (T. Clackson and H. B. Lowman, Eds.), pp 27-41, Oxford University Press.
Skelton, N. J., Koehler, M. F. T., Zobel, K., Wong, W. L., Yeh,
S., Pisabarro, M. T., Yin, J. P., Lasky, L. A. & Sidhu,
S. S. (2003) Origins of PDZ domain ligand specificity:
Structure determination and mutagenesis of the Erbin PDZ domain.
J. Biol. Chem. 278, 7645-54.
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Sidhu, S. S., Bader, G. D. & Boone, C. (2003)
Functional genomics of intracellular peptide recognition domains
with combinatorial biology methods. Curr. Opin. Chem. Biol. 7,
97-102.
Abstract
on PubMed
Sidhu, S. S., Fairbrother, W. J. & Deshayes, K.
(2003) Exploring protein-protein interactions with phage
display. Chembiochem 4, 14-25. Cover feature.
Abstract
on PubMed
Sidhu, S. S. & Weiss, G. A. (2002). DNA-encoded peptide libraries and drug discovery. In “Anticancer drug development” (B. Baguley and D. Kerr, Eds.), pp 237-248, Academic Press, San Diego.
Roth, T. A., Weiss, G. A., Eigenbrot, C. & Sidhu, S. S.
(2002). A minimized M13 coat protein defines the requirements
for assembly into the bacteriophage particle. J. Mol. Biol. 322,
357-67.
Abstract
on PubMed
Laura, R. P., Witt, A. S., Held, H. A., Gerstner, R., Deshayes,
K., Koehler, M. F. T., Kosik, K. S., Sidhu, S. S. &
Lasky, L. A. (2002). The Erbin PDZ domain binds with high
affinity and specificity to the carboxyl termini of d-catenin
and ARVCF. J. Biol. Chem. 277, 12906-14.
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Vajdos, F. F., Adams, C. W., Breece, T. N., Presta, L. G., de
Vos, A. M. & Sidhu, S. S. (2002). Comprehensive
functional maps of the antigen-binding site of an anti-ErbB2
antibody obtained with shotgun scanning mutagenesis. J. Mol.
Biol. 320, 415-28.
Abstract
on PubMed
Deshayes, K., Schaffer, M., Skelton, N. J., Nakamura, G.,
Kadkhodayan, S. & Sidhu, S. S. (2002). Rapid
identification of small binding motifs with high-throughput
phage display: Discovery of peptidic antagonists of IGF-1. Chem.
Biol. 9, 495-505.
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Sidhu, S. S. (2001). Getting what you want from phage display. Trends Microbiol. 9, 565.
Sidhu, S. S. (2001). Phage display: Increasing the
rewards from genomic information. Drug Discov. Today 6, 936.
Abstract
on PubMed
Sidhu, S. S. (2001). Engineering M13 for phage display.
Biomol. Eng. 18, 57-63.
Abstract
on PubMed
Pelletier, J. & Sidhu, S. S. (2001). Mapping
protein-protein interactions with combinatorial biology methods.
Curr. Opin. Biotechnol. 12, 340-7.
Abstract
on PubMed
Sidhu, S. S. (2000). Phage display in pharmaceutical
biotechnology. Curr. Opin. Biotechnol. 11, 610-6.
Abstract
on PubMed
Fuh, G. & Sidhu, S. S. (2000). Efficient phage
display of polypeptides fused to the carboxy-terminus of the M13
gene-3 minor coat protein. FEBS Lett. 480, 231-4.
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Weiss, G. A., Watanabe, C., Zhong, A., Goddard A. & Sidhu, S. S. (2000). Rapid mapping of protein functional epitopes
by combinatorial alanine-scanning. Proc. Natl. Acad. Sci. U.S.A.
97, 8950-4.
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Fuh, G., Pisabarro, M. T., Li, Y., Quan, C., Lasky, L. A. &
Sidhu, S. S. (2000). Analysis of PDZ domain-ligand
interactions using carboxyl-terminal phage display. J. Biol.
Chem. 275, 21486-91.
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Weiss, G. A. & Sidhu, S. S. (2000). Design and
evolution of artificial M13 coat proteins. J. Mol. Biol. 300,
213-9.
Abstract
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Weiss, G. A., Wells, J. A. & Sidhu, S. S. (2000).
Mutational analysis of the major coat protein of M13 identifies
residues that control protein display. Protein Sci. 9, 647-54.
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Sidhu, S. S., Weiss, G. A. & Wells, J. A. (2000).
High copy display of large proteins on phage for functional
selections. J. Mol. Biol. 296, 487-95.
Abstract
on PubMed
Sidhu, S. S., Lowman, H. B., Cunningham, B. C. &
Wells, J. A. (2000). Phage display for selection of novel
binding peptides. Methods Enzymol. 328, 333-63.
Abstract
on PubMed
Baardsnes, J., Sidhu, S. S., Macleod, A., Elliott, J.,
Morden, D., Watson, J. & Borgford, T. J. (1998).
Streptomyces griseus protease B - Secretion correlates with the
length of the propeptide. J. Bacteriol. 180, 3241-4.
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Sidhu, S. S. & Borgford T. J. (1996). Selection of
Streptomyces griseus protease B mutants with desired alterations
in primary specificity using a library screening strategy. J.
Mol. Biol. 257, 233-45.
Abstract
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Sidhu, S. S., Kalmar, G. B., Willis, L. G. &
Borgford, T. J. (1995). Protease evolution in Streptomyces
griseus: Discovery of a novel dimeric enzyme. J. Biol. Chem.
270, 7594-600.
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Sidhu, S. S., Kalmar, G. B., Willis, L. G. &
Borgford, T. J. (1994). Streptomyces griseus protease C: A novel
enzyme of the chymotrypsin superfamily. J. Biol. Chem. 269,
20167-71.
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Sidhu, S. S., Kalmar, G. B. & Borgford, T. J.
(1993). Characterization of the gene encoding the glutamic
acid-specific protease of Streptomyces griseus. Biochem. Cell
Biol. 71, 454-61.
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