Donnelly Centre for Cellular and Biomolecular Research   University of Toronto   Canada

Publications

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Book

Phage Display in Biotechnology and Drug Discovery

Edited by Sachdev S. Sidhu, CRC Press, New York.

A seventeen chapter volume that details the theories, principles, and methods impacting the field and demonstrates applications for peptide phage display, protein phage display, and the development of novel antibodies.

Until recently, the only source for information on the impact of phage display technology on drug discovery research has been laboratory manuals. A thorough reference guide and textbook, Phage Display in Biotechnology and Drug Discovery changes that scenario. It presents the theory and methods behind phage display technology, applications for peptide phage display, protein phage display, and the crucial role of phage display in the development of antibodies.

Highlighting the role that phage display has and will continue to play in the discovery and development of protein therapeutics, this book provides a comprehensive overview that will excite anyone interested in recombinant antibodies.

Year 2014

Characterizing WW Domain Interactions of Tumor Suppressor WWOX Reveals its Association with Multiprotein Networks.

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.

J. Biol. Chem. 28, 8865-80. (2014)

Abstract on PubMed

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes.

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.

Proc. Natl. Acad. Sci. USA 111, 2542-7. (2014)

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Design and generation of synthetic antibody libraries for phage display.

Chen, G. & Sidhu, S. S.

Methods Mol. Biol. 1131, 113-31. (2014)

Abstract on PubMed

Intracellular Routing in Breast Cancer Cells of Streptavidin-Conjugated Trastuzumab Fab Fragments Linked to Biotinylated Doxorubicin-Functionalized Metal Chelating Polymers.

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.

Biomacromolecules 15, 715-25. (2014)

Abstract on PubMed

Peptide binding properties of the three PDZ domains of bazooka (Drosophila par-3).

Yu, C. G., Tonikian. R., Felsensteiner, C., Jhingree, J. R., Desveaux, D., Sidhu, S. S. & Harris, T. J.

PLoS One 9, e86412. (2014)

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E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.

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.

Nat. Chem. Biol. 10, 156-63. (2014)

Abstract on PubMed

Development of inhibitors in the ubiquitin cascade.

Zhang, W. & Sidhu, S. S.

FEBS Lett. 588, 356-67. (2014)

Abstract on PubMed

Year 2013

Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region.

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.

Proc. Natl. Acad. Sci. USA 110, 17832-7. (2013)

Abstract on PubMed

Recombinant genetic libraries and human monoclonal antibodies.

Adams, J. J., Nelson, B. & Sidhu, S. S.

Methods Mol. Biol. 1060, 149-70. (2013)

Abstract on PubMed

Targeting HER2+ breast cancer cells: Lysosomal accumulation of anti-HER2 antibodies is influenced by antibody binding site and conjugation to polymeric nanoparticles.

Owen, S. C., Patel, N., Logie, J., Pan, G., Persson, H., Moffat, J., Sidhu, S. S. & Shoichet, M. S.

J. Control. Release 172, 395-404. (2013)

Abstract on PubMed

Engineering ubiquitin to modulate the ubiquitin proteasome system.

Ernst, A. & Sidhu, S. S.

Cell Cycle 12, 1651-2. (2013)

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The erythropoietin receptor is a downstream effector of Klotho-induced cytoprotection.

Hu, M.-C., Shi, M., Cho, H. J., Zhang, J., Pavlenco, A., Sidhu, S. S., Huang, L. J.-S. & Moe, O. W.

Kidney Int. 84, 468-81. (2013)

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SH3 interactome conserves general function over specific form.

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.

Mol. Syst. Biol. 9, 652. (2013)

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Design of Synthetic Autonomous VH Domain Libraries and Structural Analysis of a VH Domain Bound to Vascular Endothelial Growth Factor.

Ma, X., Barthelemy, P. A., Rouge, L., Wiesmann, C. & Sidhu, S. S.

J. Mol. Biol. 425, 2247-59. (2013)

Abstract on PubMed

Interaction domains of Sos1/Grb2 are finely tuned for cooperative control of embryonic stem cell fate.

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.

Cell 152, 1008-20. (2013)

Abstract on PubMed

Engineering and analysis of peptide-recognition domain specificities by phage display and deep sequencing.

McLaughlin, M. E. & Sidhu, S. S.

Methods Enzymol. 523, 327-49. (2013)

Abstract on PubMed

A Strategy for Modulation of Enzymes in the Ubiquitin System.

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.

Science 339, 590-5. (2013)

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Deciphering the molecular bases of the biological effects of antibodies against Interleukin-2: a versatile platform for fine epitope mapping.

Rojas, G., Pupo, A., Leon, K., Avellanet, J., Carmenate, T. & Sidhu, S.

Immunobiology 218, 105-13. (2013)

Abstract on PubMed

Year 2012

CDR-H3 Diversity is Not Required For Antigen Recognition by Synthetic Antibodies.

Persson, H., Ye, W., Wernimont, A., Adams, J. J., Lam, R. & Sidhu, S. S.

J. Mol. Biol. 425, 803-11. (2012)

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KIF14 negatively regulates Rap1a-Radil signaling during breast cancer progression.

Ahmed, S. M., Thériault, B. L., Uppalapati, M., Chiu, C. W., Gallie, B. L., Sidhu, S. S. & Angers, S.

J. Cell Biol. 199, 951-67. (2012)

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Immunology: Evolving superkines for selectivity.

Miersch, S. & Sidhu, S. S.

Nat. Chem. Biol. 8, 955-6. (2012)

Abstract on PubMed

Two synthetic antibodies that recognize and neutralize distinct proteolytic forms of the Ebola virus envelope blycoprotein.

Koellhoffer, J. F., Chen, G., Sandesara, R. G., Bale, S., Ollmann Saphire, E., Chandran, K., Sidhu, S. S. & Lai, J. R.

Chembiochem 13 2549-57. (2012)

Abstract on PubMed

A short DNA aptamer that recognizes TNF-alpha and blocks its activity in vitro.

Orava, E. W., Jarvik, N., Shek, Y. L., Sidhu, S. S. & Gariepy, J.

ACS Chem. Biol. 8 170-8. (2012)

Abstract on PubMed

Superbinder SH2 Domains Act as Antagonists of Cell Signaling.

Kaneko, T., Huang, H., Cao, X., Li, X., Li, C., Voss, C., Sidhu, S. S. & Li, S. S.

Sci. Signal. 5, ra68. (2012)

Abstract on PubMed

Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography.

Mandal, K., Uppalapati, M., Ault-Riché, D., Kenney, J., Lowitz, J., Sidhu, S. S. & Kent, S. B.

Proc. Natl. Acad. Sci. USA 109, 14779-84. (2012)

Abstract on PubMed

T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment.

Miller, K. R., Koide, A., Leung, B., Fitzsimmons, J., Yoder, B., Yuan, H., Jay, M., Sidhu, S. S., Koide, S. & Collins, E. J.

PLoS One 7, e43746. (2012)

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Selecting and Purifying Autonomous Human Variable Heavy (VH) Domains.

Tonikian, R., & Sidhu, S. S.

Methods Mol. Biol. 911, 327-53. (2012)

Abstract on PubMed

Conformational Control of the Ste5 Scaffold Protein Insulates Against MAP Kinase Misactivation.

Zalatan, J. G., Coyle, S. M., Rajan, S., Sidhu, S. S. & Lim, W. A.

Science 337, 1218-22. (2012)

Abstract on PubMed

Synthetic antibodies - concepts, practical considerations and potential.

Miersch, S. & Sidhu, S. S.

Methods 57, 486-98. (2012)

Abstract on PubMed

Synthetic antibody libraries.

Nelson, B. & Sidhu, S. S.

Methods Mol. Biol. 899, 27-41. (2012)

Abstract on PubMed

Recombinant antibodies and in vitro selection technologies.

Geyer, C. R., McCafferty, J., Dübel, S., Bradbury, A. R. & Sidhu, S. S.

Methods Mol. Biol. 901, 11-32. (2012)

Abstract on PubMed

Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains.

Teyra, J., Sidhu, S. S. & Kim, P. M.

FEBS Lett. 586, 2631-7. (2012)

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Antibodies for All: The Case for Genome-wide Affinity Reagents.

Sidhu, S. S.

FEBS Lett. 586, 2778-9. (2012)

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Synthetic human monoclonal antibodies towards staphylococcal enterotoxin B (SEB) protective against toxic shock syndrome.

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.
* equal contribution

J. Biol. Chem. 287, 25203-15. (2012)

Abstract on PubMed

Synthetic antibodies as tools to probe RNA-binding protein function.

Laver, J. D., Ancevicius, K., Sollazzo, P., Westwood, J. T., Sidhu, S. S., Lipshitz, H. D. & Smibert, C. A.

Molec. Biosyst. 8, 1650-7. (2012)

Abstract on PubMed

Deciphering the molecular bases of the biological effects of antibodies against Interleukin-2: a versatile platform for fine epitope mapping.

Rojas, G., Pupo, A., Leon, K., Avellanet, J., Carmenate, T. & Sidhu, S. S.

Immunobiol., [in press]

Abstract on PubMed

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.

Kim, T., Tyndel, M. S., Huang, H., Sidhu, S. S., Bader, G. D., Gfeller, D. & Kim, P. M.

Nucl. Acids Res. 40, e47. (2012)

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Charged and hydrophobic surfaces on the a chain of shiga-like toxin 1 recognize the C-terminal domain of ribosomal stalk proteins.

McCluskey, A. J., Bolewska-Pedyczak, E., Jarvik, N., Chen, G., Sidhu, S. S. & Gariépy, J.

PLoS One 7, e31191. (2012)

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Simplified synthetic antibody libraries.

Rajan, S. & Sidhu, S. S.

Methods Enzymol. 502, 3-23. (2012)

Abstract on PubMed

Year 2011

Studying binding specificities of peptide recognition modules by high-throughput phage display selections.

Huang, H. & Sidhu, S. S.

Methods Mol. Biol. 781, 87-97. (2011)

Abstract on PubMed

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps.

Yip, K.Y., Utz, L., Sitwell, S., Hu, X., Sidhu, S. S., Turk, B. E., Gerstein, M. B. & Kim, P. M.

BMC Biol. 9, 53. (2011)

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Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): Identification of selective inhibitors of collagenase-1 (MMP-1).

Bahudhanapati, H., Zhang, Y., Sidhu, S. S. & Brew, K.

Biol. Chem. 286, 31761-70. (2011)

Abstract on PubMed

A roadmap to generate renewable protein binders to the human proteome.

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.

Nat. Methods 8, 551-8. (2011)

Abstract on PubMed

The multiple-specificity landscape of modular peptide recognition domains.

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.

Mol. Syst. Biol. 7, 484. (2011)

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Development of reagents and assays for the detection of pathogenic Burkholderia species.

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.

Faraday Discuss. 149, 23-36. (2011)

Abstract on PubMed

Beyond natural antibodies: the power of in vitro display technologies.

Bradbury, A. R., Sidhu, S. S., Dübel, S., & McCafferty, J.

Nat. Biotechnol. 29, 245-54. (2011)

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Evolving specificity from variability for protein interaction domains.

Kaneko, T., Sidhu, S. S. & Li, S. S.

Trends Biochem. Sci. 36, 183-90. (2011)

Abstract on PubMed

A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.

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.

Nat. Struct. Mol. Biol. 18, 100-6. (2011)

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Year 2010

Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling.

Oka, T., Remue, E., Meerschaert, K., Vanloo, B., Boucherie, C., Gfeller, D., Bader, G. D., Sidhu, S. S., Vandekerckhove, J., Gettemans, J. & Sudol, M.

Biochem. J. 432, 461-72. (2010)

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Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing.

Ernst, A., Gfeller, D., Kan, Z., Seshagiri, S., Kim, P. M., Bader, G. D. & Sidhu, S. S.

Mol. Biosyst. 6, 1782-90. (2010)

Abstract on PubMed

Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine.

Fisher, R. D., Ultsch, M., Lingel, A., Schaefer, G., Shao, L., Birtalan, S., Sidhu, S. S. & Eigenbrot, C.

J. Mol. Biol. 402, 217-29. (2010)

Abstract on PubMed

MOTIPS: Automated motif analysis for predicting targets of modular protein domains.

Lam, H. Y. K., Kim, P. M., Mok, J., Tonikian, R., Sidhu, S. S., Turk, B. E., Snyder, M. & Gerstein, M. B.

BMC Bioinformatics 11, 243. (2010)

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The functional capacity of the natural amino acids for molecular recognition.

Birtalan, S., Fisher, R. D. & Sidhu, S. S.

Mol. Biosyst. 6, 1186-94. (2010)

Abstract on PubMed

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Year 2009

Mapping protein function by combinatorial mutagenesis.

Pal, G. & Sidhu, S. S.

In "Computational protein-protein interactions" (R. Nussinov & G. Schreiber, Eds), pp 57-86, CRC Press: Boca Raton, FL. (2009)

Phage display.

Ernst, A. & Sidhu, S. S.

In "Protein Engineering and Design" (S. Park and J. Cochran, Eds), pp 1-22, Taylor and Francis: Boca Raton. (2009)

Improving therapeutic efficacy of a complement receptor by structure-based affinity maturation.

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.

J. Biol. Chem. 284, 35605-11. (2009)

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Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

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.

PLoS Biol. 7, e1000218. (2009)

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Rapid evolution of functional complexity in a domain family.

Ernst, A., Sazinsky, S. L., Hui, S., Currell, B., Dharsee, M., Seshagiri, S., Bader, G. D. & Sidhu, S. S.

Sci. Signal. 2, ra50. (2009)

Abstract on PubMed

Crystal structure of full-length KcsA in its closed conformation.

Uysal, S., Vasquez, V., Esaiki, K.,Fellouse, F. A., Sidhu, S. S., Koide, S., Perozo, E. & Kossiakoff, A. A.

Proc. Natl. Acad. Sci. USA 106, 6644-9. (2009)

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The importance of being tyrosine: Lessons in molecular recognition from minimalist synthetic binding proteins.

Koide, S. & Sidhu, S. S.

ACS Chem. Biol. 4, 325-34. (2009)

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Inhibition of Wnt/β-catenin signaling by peptides that target dishevelled PDZ domains.

Zhang, Y., Appleton, B. A., Wiesmann, C., Lau, T., Costa, M., Hannoush, R. N. & Sidhu, S. S.

Nat. Chem. Biol. 5, 217-9. (2009)

Abstract on PubMed

Two-state selection of conformation-specific antibodies.

Gao, J., Sidhu, S. S. & Wells, J. A.

Proc. Natl. Acad. Sci. USA 106, 3071-6. (2009)

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Year 2008

A specificity map for the PDZ domain family.

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.

PLoS Biol. 6, 2043-59. (2008)

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Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.

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.

Cell 134, 668-78. (2008)

Abstract on PubMed

A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces.

Gilbreth, R. N., Esaki, K., Koide, A., Sidhu, S. S. & Koide, S.

J. Mol. Biol. 381, 407-18. (2008)

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Submitting antibodies to binding arbitration.

Michnick, S. W. & Sidhu, S. S.

Nat. Chem. Biol. 4, 326-29. (2008)

Abstract on PubMed

Regulation of a late phase of T cell polarity and effector functions by Crtam.

Yeh, J.-H., Sidhu, S. S. & Chan, A. C.

Cell 132, 846-59. (2008)

Abstract on PubMed

The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies.

Birtalan, S., Zhang, Y., Fellouse, F. A., Shao, L., Schaefer, G. & Sidhu, S. S.

J. Mol. Biol. 337, 1518-28. (2008)

Abstract on PubMed

Comprehensive analysis of the factors contributing to the stability and solubility of autonomous human VH domains.

Barthelemy, P. A., Raab, H., Appleton, B. A., Bond, C. J., Wu, P., Wiesmann, C. & Sidhu, S. S.

J. Biol. Chem. 138, 3639-54. (2008)

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Synthetic antibodies for specific recognition and crystallization of structured RNA.

Ye, J.-D., Tereshko, V., Frederiksen, J. K., Koide, A., Fellouse, F. A., Sidhu, S. S., Koide, S., Kossiakoff, A. A. & Piccirilli, J. A.

Proc. Natl. Acad. Sci. USA. 105, 82-7. (2007)

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Year 2007

The type III effector EspF coordinates membrane trafficking by the spatiotemporal activation of two eukaryotic signaling pathways.

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.

1J. Cell Biol. 78, 1265-78. (2007)

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Phage display for engineering and analyzing protein interaction interfaces.

Sidhu, S. S. & Koide, S.

Curr. Opin. Struct. Biol. 17, 481-7. (2007)

Abstract on PubMed

High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries.

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.

J. Mol. Biol. 373, 924-40. (2007)

Abstract on PubMed

Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3.

Runyon, S. T., Zhang, Y., Appleton, B. A., Sazinsky, S. L., Wu, P., Pan, B., Wiesmann, C., Skelton, N. J. & Sidhu, S. S.

Protein Sci. 16, 2454-71. (2007)

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Structural and functional analysis of the ligand specificity of the HtrA2/Omi PDZ domain.

Zhang, Y., Appleton, B. A., Wu, P., Wiesmann, C. & Sidhu, S. S.

Protein Sci. 16, 1738-50. (2007)

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Identifying specificity profiles for peptide binding modules with phage-displayed peptide libraries.

Tonikian, R., Zhang, Y., Boone, C. & Sidhu, S. S.

Nat. Protoc. 2, 1368-86. (2007)

Abstract on PubMed

Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.

Gupta, R., Kus, B., Fladd, C., Wasmuth, J., Tonikian, R., Sidhu, S. S., Krogan, N. J., Parkinson, J. & Rotin, D.

Mol. Syst. Biol. 3, 116. (2007)

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Exploring and designing protein function with restricted diversity.

Sidhu, S. S. & Kossiakoff, A. A.

Curr. Opin. Chem. Biol. 11, 347-54. (2007)

Abstract on PubMed

Full-length antibodies on display.

Sidhu, S. S.

Nat. Biotechnol. 25, 537-8. (2007)

Abstract on PubMed

Making antibodies in bacteria.

Fellouse, F. A. & Sidhu, S. S.

In "Making and using antibodies" (G. C. Howard & M. R. Kaser, Eds.), pp 157-180, CRC Press, Boca Raton, FL. (2007)

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Year 2006

Synthetic therapeutic antibodies.

Sidhu, S. S. & Fellouse, F. A.

Nat. Chem. Biol. 12, 682-88. (2006)

Abstract on PubMed

Engineering the M13 bacteriophage coat protein for improved phage display.

Sidhu, S. S., Feld, B. K. & Weiss, G. A.

In "Methods in molecular biology, volume 352: Protein engineering protocols" (K. M. Arndt and K. M. Muller, Eds.), pp 205-19, Humana Press Inc., Totowa, NJ. (2006)

Activation of the proapoptotic death receptor DR5 by oligomeric peptide and antibody agonists.

Li, B., Totpal, K., Russell, S., Yeh, S., Wong, W. L., Cochran, A., Ashkenazi, A., Hymowitz, S & Sidhu, S. S.

J. Mol. Biol. 361, 522-36. (2006)

Abstract on PubMed

Comprehensive and Quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning.

Pal, G., Kouadio, J.-L., Artis, D. R., Kossiakoff, A. A. & Sidhu, S. S.

J. Biol. Chem. 281, 22378-85. (2006)

JBC paper of the week. Cover feature in ASBMB Today (October, 2006).

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Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1: Insights into determinants of PDZ domain specificity.

Appleton, B. A., Zhang, Y., Wu, P., Yin, J. P., Hunziker, W., Skelton, N. J. Sidhu, S. S. & Wiesmann, C.

J. Biol. Chem. 281, 22312-20. (2006)

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Convergent and divergent ligand specificity amongst the PDZ domains of the LAP and zonula occludens (ZO) families.

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.

J. Biol. Chem. 281, 22299-311. (2006)

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Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code.

Fellouse, F. A., Barthelemy, P. A., Kelley, R. F. & Sidhu, S. S.

J. Mol. Biol. 357, 100-14. (2006)

Abstract on PubMed

Synthetic antibody libraries.

Fellouse, F. A. & Sidhu, S. S.

In "Phage display in drug discovery and Biotechnology" (S. S. Sidhu, Ed.), pp 709-740. CRC Press, Boca Raton, FL. (2006)

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Year 2005

Alternative views of functional protein binding epitopes obtained by combinatorial shotgun scanning mutagenesis.

Pal, G., Fong, S.-Y., Kossiakoff, A. A. & Sidhu, S. S.

Protein Sci. 14, 2405-13. (2005)

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Molecular recognition by a binary code.

Fellouse, F. A., Peden, A. A. & Sidhu, S. S.

J. Mol. Biol. 348, 1153-62. (2005)

Cover feature.

Abstract on PubMed

A structure-based database of antibody variable domain diversity.

Bond, C., Wiesmann, C., Marsters, J. C. & Sidhu, S. S.

J. Mol. Biol. 348, 699-709. (2005)

Abstract on PubMed

Intramolecular cooperativity in a protein binding site assessed by combinatorial shotgun scanning mutagenesis

Pal, G., Ultsch, M. H., Clark, P. C., Currell, B., Kossiakoff, A. A. & Sidhu, S. S.

J. Mol. Biol. 347, 489-94. (2005)

Abstract on PubMed

PDZ domains: Intracellular mediators of carboxy-terminal protein recognition and scaffolding.

Lasky, L. A., Skelton, N. J. & Sidhu, S. S.

In "Modular protein domains" (G. Cesarini, M. Gimona, M. Sudol & M. Yaffe, Eds.), pp 257-278, Wiley-VCH Inc., Germany. (2005)

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Year 2004

Synthetic antibodies from a four amino acid code: A dominant role for tyrosine in antigen recognition.

Fellouse, F. A., Wiesmann, C. & Sidhu, S. S.

Proc. Natl. Acad. Sci. USA 101, 12467-72. (2004)

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High affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold.

Lee, C. V., Liang, W.-C., Dennis, M. S., Eigenbrot, C., Sidhu, S. S. & Fuh, G.

J. Mol. Biol. 340, 1073-93. (2004)

Abstract on PubMed

Phage display-derived peptide-binding provides structural insight into insulin-like growth factor I function.

Skelton, N. J., Schaffer, M. L., Deshayes, K., Blandl, T., Runyon, S., Nakamura, G. & Sidhu, S. S.

Spectroscopy 18, 237-49. (2004)

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Comprehensive mutational analysis of the M13 major coat protein: Improved scaffolds for C-terminal phage display.

Held, H. A. & Sidhu, S. S.

J. Mol. Biol. 340, 587-97. (2004)

Abstract on PubMed

Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions.

Sidhu, S. S., Li, B., Chen, Y., Fellouse, F. A., Eigenbrot, C. & Fuh, G.

J. Mol. Biol. 338, 299-310. (2004)

Abstract on PubMed

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Bivalent antibody phage display mimics natural immunoglobulin.

Lee, C. V., Sidhu, S. S. & Fuh, G.

J. Immunol. Methods 284, 119-32. (2004)

Abstract on PubMed

Definition of the consensus motif recognized by gamma-adaptin ear domains.

Mattera, R., Ritter, B., Sidhu, S. S., McPherson, P. S. & Bonifacino, J. S.

J. Biol. Chem. 279, 8018-28. (2004)

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Year 2003

Comprehensive mutagenesis of the C-terminal domain of the M13 gene-3 minor coat protein: The requirements for assembly into the bacteriophage particle.

Weiss, G. A., Roth, T. A., Baldi, P. F. & Sidhu, S. S.

J. Mol. Biol. 332, 777-82. (2003)

Abstract on PubMed

Complex with a phage display-derived peptide provides insight into the function of insulin-like growth factor I.

Schaffer, M. L., Deshayes, K., Nakamura, G. R., Sidhu, S. S. & Skelton, N. J.

Biochem. 42, 9324-34. (2003)

Abstract on PubMed

Contributions of CDR3 to VHH domain stability and the design of monobody scaffolds for naïve antibody libraries.

Bond, C., Marsters, J. C. Jr. & Sidhu, S. S.

J. Mol. Biol. 332, 643-55. (2003)

Abstract on PubMed

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.

Pal, G., Kossiakoff, A. A., Sidhu, S. S.

J. Mol. Biol. 332, 195-204. (2003)

Abstract on PubMed

Constructing phage display libraries by oligonucleotide-directed mutagenesis.

Sidhu, S. S. & Weiss, G. A.

In "Phage display: A practical approach" (T. Clackson and H. B. Lowman, Eds.), pp 27-41, Oxford University Press. (2003)

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Origins of PDZ domain ligand specificity: Structure determination and mutagenesis of the Erbin PDZ domain.

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.

J. Biol. Chem. 278, 7645-54. (2003)

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Functional genomics of intracellular peptide recognition domains with combinatorial biology methods.

Sidhu, S. S., Bader, G. D. & Boone, C.

Curr. Opin. Chem. Biol. 7, 97-102. (2003)

Abstract on PubMed

Exploring protein-protein interactions with phage display.

Sidhu, S. S., Fairbrother, W. J. & Deshayes, K.

Chembiochem. 4, 14-25. (2003)

Cover feature.

Abstract on PubMed

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Year 2002

DNA-encoded peptide libraries and drug discovery.

Sidhu, S. S. & Weiss, G. A.

In "Anticancer drug development" (B. Baguley and D. Kerr, Eds.), pp 237-48, Academic Press, San Diego. (2002)

A minimized M13 coat protein defines the requirements for assembly into the bacteriophage particle.

Roth, T. A., Weiss, G. A., Eigenbrot, C. & Sidhu, S. S.

J. Mol. Biol. 322, 357-67. (2002)

Abstract on PubMed

The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of δ-catenin and ARVCF.

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.

J. Biol. Chem. 277, 12906-14. (2002)

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Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis.

Vajdos, F. F., Adams, C. W., Breece, T. N., Presta, L. G., de Vos, A. M. & Sidhu, S. S.

J. Mol. Biol. 320, 415-28. (2002)

Abstract on PubMed

Rapid identification of small binding motifs with high-throughput phage display: Discovery of peptidic antagonists of IGF-1.

Deshayes, K., Schaffer, M., Skelton, N. J., Nakamura, G., Kadkhodayan, S. & Sidhu, S. S.

Chem. Biol. 9, 495-505. (2002)

Abstract on PubMed

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Year 2001

Getting what you want from phage display.

Sidhu, S. S.

Trends Microbiol. 9, 565. (2001)

Phage display: Increasing the rewards from genomic information.

Sidhu, S. S.

Drug Discov. Today 6, 936. (2001)

Abstract on PubMed

Engineering M13 for phage display.

Sidhu, S. S.

Biomol. Eng. 18, 57-63. (2001)

Abstract on PubMed

Mapping protein-protein interactions with combinatorial biology methods.

Pelletier, J. & Sidhu, S. S.

Curr. Opin. Biotech. 12, 340-7. (2001)

Abstract on PubMed

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Year 2000 and Earlier

Phage display in pharmaceutical biotechnology.

Sidhu, S. S.

Curr. Opin. Biotechnol. 11, 610-6. (2000)

Abstract on PubMed

Phage display for selection of novel binding peptides.

Sidhu, S. S., Lowman, H. B., Cunningham, B. C. & Wells, J. A.

Methods Enzymol. 328, 333-63. (2000)

Abstract on PubMed

Efficient phage display of polypeptides fused to the carboxy-terminus of the M13 gene-3 minor coat protein.

Fuh, G. & Sidhu, S. S.

FEBS Lett. 480, 231-4. (2000)

Abstract on PubMed

Rapid mapping of protein functional epitopes by combinatorial alanine scanning.

Weiss, G. A., Watanabe, C., Zhong, A., Goddard A. & Sidhu, S. S.

Proc. Natl. Acad. Sci. U.S.A. 97, 8950-4. (2000)

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Analysis of PDZ domain-ligand interactions using carboxyl-terminal phage display.

Fuh, G., Pisabarro, M. T., Li, Y., Quan, C., Lasky, L. A. & Sidhu, S. S.

J. Biol. Chem. 275, 21486-91. (2000)

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Design and evolution of artificial M13 coat proteins.

Weiss, G. A. & Sidhu, S. S.

J. Mol. Biol. 300, 213-9. (2000)

Abstract on PubMed

Mutational analysis of the major coat protein of M13 identifies residues that control protein display.

Weiss, G. A., Wells, J. A. & Sidhu, S. S.

Protein Sci. 9, 647-54. (2000)

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High copy display of large proteins on phage for functional selections.

Sidhu, S. S., Weiss, G. A. & Wells, J. A.

J. Mol. Biol. 296, 487-95. (2000)

Abstract on PubMed

Streptomyces griseus protease B - Secretion correlates with the length of the propeptide.

Baardsnes, J., Sidhu, S., Macleod, A., Elliott, J., Morden, D. Watson, J. & Borgford, T.

J. Bacteriol. 180, 3241-4. (1998)

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Selection of Streptomyces griseus protease B mutants with desired alterations in primary specificity using a library screening strategy.

Sidhu, S. S. & Borgford T. J.

J. Mol. Biol. 257, 233-45. (1996)

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Protease evolution in Streptomyces griseus: Discovery of a novel dimeric enzyme.

Sidhu, S. S., Kalmar, G. B., Willis, L. G. & Borgford, T. J.

J. Biol. Chem. 270, 7594-600. (1995)

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Streptomyces griseus protease C: A novel enzyme of the chymotrypsin superfamily.

Sidhu, S. S., Kalmar, G. B., Willis, L. G. & Borgford, T. J.

J. Biol. Chem. 269, 20167-71. (1994)

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Characterization of the gene encoding the glutamic-acid-specific protease of Streptomyces griseus.

Sidhu, S. S., Kalmar, G. B. & Borgford, T. J.

Biochem. Cell Biol. 71, 454-61. (1993)

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Last Modified 8 March, 2012