Abstract
The precise and unambiguous elucidation and characterization of interactions between a high affinity recognition entity and its cognate protein provides important insights for the design and development of drugs with optimized properties and efficacy. In oncology, one important target protein has been shown to be the epidermal growth factor receptor (EGFR) through the development of therapeutic anticancer antibodies that are selective inhibitors of EGFR activity. More recently, smaller protein derived from the 10th type III domain of human fibronectin termed an adnectin has also been shown to inhibit EGFR in clinical studies. The mechanism of EGFR inhibition by either an adnectin or an antibody results from specific binding of the high affinity protein to the extracellular portion of EGFR (exEGFR) in a manner that prevents phosphorylation of the intracellular kinase domain of the receptor and thereby blocks intracellular signaling. Here, the structural changes induced upon binding were studied by probing the solution conformations of full length exEGFR alone and bound to a cognate adnectin through hydrogen/deuterium exchange mass spectrometry (HDX MS). The effects of binding in solution were identified and compared with the structure of a bound complex determined by X-ray crystallography.
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Harari, P.M.: Epidermal growth factor receptor inhibition strategies in oncology. Endocrinol. Relat. Cancer 11, 689–708 (2004)
Lemmon, M.A.: Ligand-induced ErbB receptor dimerization. Exp. Cell Res. 315, 638–648 (2009)
Ferguson, K.M.: Structure-based view of epidermal growth factor receptor regulation. Annu. Rev. Biophys. 37, 353–373 (2008)
Ramamurthy, V., Krystek Jr., S.R., Bush, A., Wei, A., Emanuel, S.L., Das Gupta, R., Janjua, A., Cheng, L., Murdock, M., Abramczyk, B., Cohen, D., Lin, Z., Morin, P., Davis, J.H., Dabritz, M., McLaughlin, D.C., Russo, K.A., Chao, G., Wright, M.C., Jenny, V.A., Engle, L.J., Furfine, E., Sheriff, S.: Structures of adnectin/protein complexes reveal an expanded binding footprint. Structure 20, 259–269 (2012)
Ogiso, H., Ishitani, R., Nureki, O., Fukai, S., Yamanaka, M., Kim, J.H., Saito, K., Sakamoto, A., Inoue, M., Shirouzu, M., Yokoyama, S.: Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell 110, 775–787 (2002)
Arkhipov, A., Shan, Y., Das, R., Endres, N.F., Eastwood, M.P., Wemmer, D.E., Kuriyan, J., Shaw, D.E.: Architecture and membrane interactions of the EGF receptor. Cell 152, 557–569 (2013)
Shan, Y., Eastwood, M.P., Zhang, X., Kim, E.T., Arkhipov, A., Dror, R.O., Jumper, J., Kuriyan, J., Shaw, D.E.: Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell 149, 860–870 (2012)
Sherrill, J.M., Kyte, J.: Activation of epidermal growth factor receptor by epidermal growth factor. Biochemistry 35, 5705–5718 (1996)
Salomon, D.S., Brandt, R., Ciardiello, F., Normanno, N.: Epidermal growth factor-related peptides and their receptors in human malignancies. Crit. Rev. Oncol. Hematol. 19, 183–232 (1995)
Woodburn, J.R.: The epidermal growth factor receptor and its inhibition in cancer therapy. Pharmacol. Ther. 82, 241–250 (1999)
Ennis, B.W., Lippman, M.E., Dickson, R.B.: The EGF receptor system as a target for antitumor therapy. Cancer Investig. 9, 553–562 (1991)
Xu, L., Aha, P., Gu, K., Kuimelis, R.G., Kurz, M., Lam, T., Lim, A.C., Liu, H., Lohse, P.A., Sun, L., Weng, S., Wagner, R.W., Lipovsek, D.: Directed evolution of high-affinity antibody mimics using mRNA display. Chem. Biol. 9, 933–942 (2002)
Lipovsek, D.: Adnectins: engineered target-binding protein therapeutics. Protein Eng. Des. Sel. 24, 3–9 (2011)
Dickinson, C.D., Veerapandian, B., Dai, X.P., Hamlin, R.C., Xuong, N.H., Ruoslahti, E., Ely, K.R.: Crystal structure of the tenth type III cell adhesion module of human fibronectin. J. Mol. Biol. 236, 1079–1092 (1994)
Koide, A., Bailey, C.W., Huang, X., Koide, S.: The fibronectin type III domain as a scaffold for novel binding proteins. J. Mol. Biol. 284, 1141–1151 (1998)
Getmanova, E.V., Chen, Y., Bloom, L., Gokemeijer, J., Shamah, S., Warikoo, V., Wang, J., Ling, V., Sun, L.: Antagonists to human and mouse vascular endothelial growth factor receptor 2 generated by directed protein evolution in vitro. Chem. Biol. 13, 549–556 (2006)
Koide, A., Abbatiello, S., Rothgery, L., Koide, S.: Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor. Proc. Natl. Acad. Sci. U. S. A. 99, 1253–1258 (2002)
Wojcik, J., Hantschel, O., Grebien, F., Kaupe, I., Bennett, K.L., Barkinge, J., Jones, R.B., Koide, A., Superti-Furga, G., Koide, S.: A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nat. Struct. Mol. Biol. 17, 519–527 (2010)
Hackel, B.J., Kapila, A., Wittrup, K.D.: Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuffling. J. Mol. Biol. 381, 1238–1252 (2008)
Tiyanont, K., Wales, T.E., Aste-Amezaga, M., Aster, J.C., Engen, J.R., Blacklow, S.C.: Evidence for increased exposure of the Notch1 metalloprotease cleavage site upon conversion to an activated conformation. Structure 19, 546–554 (2011)
Malito, E., Faleri, A., Lo Surdo, P., Veggi, D., Maruggi, G., Grassi, E., Cartocci, E., Bertoldi, I., Genovese, A., Santini, L., Romagnoli, G., Borgogni, E., Brier, S., Lo Passo, C., Domina, M., Castellino, F., Felici, F., van der Veen, S., Johnson, S., Lea, S.M., Tang, C.M., Pizza, M., Savino, S., Norais, N., Rappuoli, R., Bottomley, M.J., Masignani, V.: Defining a protective epitope on factor H binding protein, a key meningococcal virulence factor and vaccine antigen. Proc. Natl. Acad. Sci. U. S. A. 110, 3304–3309 (2013)
Zhang, Q., Willison, L.N., Tripathi, P., Sathe, S.K., Roux, K.H., Emmett, M.R., Blakney, G.T., Zhang, H.M., Marshall, A.G.: Epitope mapping of a 95 kDa antigen in complex with antibody by solution-phase amide backbone hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 83, 7129–7136 (2011)
Pacholarz, K.J., Garlish, R.A., Taylor, R.J., Barran, P.E.: Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem. Soc. Rev. 41, 4335–4355 (2012)
Percy, A.J., Rey, M., Burns, K.M., Schriemer, D.C.: Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review. Anal. Chim. Acta 721, 7–21 (2012)
Chalmers, M.J., Busby, S.A., Pascal, B.D., West, G.M., Griffin, P.R.: Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Exp. Rev. Proteomics 8, 43–59 (2011)
Tsutsui, Y., Wintrode, P.L.: Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions. Curr. Med. Chem. 14, 2344–2358 (2007)
Kaveti, S., Engen, J.R.: Protein interactions probed with mass spectrometry. Methods Mol. Biol. 316, 179–197 (2006)
Maier, C.S., Deinzer, M.L.: Protein conformations, interactions, and H/D exchange. Methods Enzymol. 402, 312–360 (2005)
Engen, J.R., Wales, T.E., Chen, S., Marzluff, E.M., Hassell, K.M., Weis, D.D., Smithgall, T.E.: Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry. Int. Rev. Phys. Chem. 32, 96–127 (2013)
Engen, J.R.: Analysis of protein complexes with hydrogen exchange and mass spectrometry. Analyst 128, 623–628 (2003)
Wales, T.E., Engen, J.R.: Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25, 158–170 (2006)
Mandell, J.G., Baerga-Ortiz, A., Croy, C.H., Falick, A.M., Komives, E.A.: Application of amide proton exchange mass spectrometry for the study of protein–protein interactions. Curr. Protoc. Protein Sci. Chapter 20, Unit20.29 (2005)
Lerner, E.C., Trible, R.P., Schiavone, A.P., Hochrein, J.M., Engen, J.R., Smithgall, T.E.: Activation of the Src family kinase Hck without SH3-linker release. J. Biol. Chem. 280, 40832–40837 (2005)
Yan, Y., Chen, G., Wei, H., Huang, R., Mo, J., Rempel, D.L., Tymiak, A.A., Gross, M.L.: Fast photochemical oxidation of proteins (FPOP) maps the epitope of EGFR binding to adnectin. J. Am. Soc. Mass Spectrom. (2014)
Wales, T.E., Fadgen, K.E., Gerhardt, G.C., Engen, J.R.: High-speed and high-resolution UPLC separation at 0° C. Anal. Chem. 80, 6815–6820 (2008)
Iacob, R.E., Bou-Assaf, G.M., Makowski, L., Engen, J.R., Berkowitz, S.A., Houde, D.: Investigating monoclonal antibody aggregation using a combination of H/DX-MS and other biophysical measurements. J. Pharm. Sci. 102, 4315–4329 (2013)
Burkitt, W., O’Connor, G.: Assessment of the repeatability and reproducibility of hydrogen/deuterium exchange mass spectrometry measurements. Rapid Commun. Mass Spectrom. 22, 3893–3901 (2008)
Houde, D., Berkowitz, S.A., Engen, J.R.: The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J. Pharm. Sci. 100, 2071–2086 (2011)
Iacob, R.E., Engen, J.R.: Hydrogen exchange mass spectrometry: are we out of the quicksand? J. Am. Soc. Mass Spectrom. 23, 1003–1010 (2012)
Plumb, R.S., Johnson, K.A., Rainville, P., Smith, B.W., Wilson, I.D., Castro-Perez, J.M., Nicholson, J.K.: UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun. Mass Spectrom. 20, 1989–1994 (2006)
Wales, T.E., Eggertson, M.J., Engen, J.R.: Considerations in the analysis of hydrogen exchange mass spectrometry data. Methods Mol. Biol. 1007, 263–288 (2013)
Ahn, J., Cao, M.J., Yu, Y.Q., Engen, J.R.: Accessing the reproducibility and specificity of pepsin and other aspartic proteases. Biochim. Biophys. Acta 1834, 1222–1229 (2013)
Rand, K.D., Pringle, S.D., Morris, M., Engen, J.R., Brown, J.M.: ETD in a traveling wave ion guide at tuned Z-spray ion source conditions allows for site-specific hydrogen/deuterium exchange measurements. J. Am. Soc. Mass Spectrom. 22, 1784–1793 (2011)
Zehl, M., Rand, K.D., Jensen, O.N., Jorgensen, T.J.: Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution. J. Am. Chem. Soc. 130, 17453–17459 (2008)
Weis, D.D., Engen, J.R., Kass, I.J.: Semi-automated data processing of hydrogen exchange mass spectra using HX-Express. J. Am. Soc. Mass Spectrom. 17, 1700–1703 (2006)
Guttman, M., Weis, D.D., Engen, J.R., Lee, K.K.: Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra. J. Am. Soc. Mass Spectrom. 24, 1906–1912 (2013)
Seeliger, D., de Groot, B.L.: Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des. 24, 417–422 (2010)
Chung, I., Akita, R., Vandlen, R., Toomre, D., Schlessinger, J., Mellman, I.: Spatial control of EGF receptor activation by reversible dimerization on living cells. Nature 464, 783–787 (2010)
Clayton, A.H., Walker, F., Orchard, S.G., Henderson, C., Fuchs, D., Rothacker, J., Nice, E.C., Burgess, A.W.: Ligand-induced dimer-tetramer transition during the activation of the cell surface epidermal growth factor receptor-A multidimensional microscopy analysis. J. Biol. Chem. 280, 30392–30399 (2005)
Low-Nam, S.T., Lidke, K.A., Cutler, P.J., Roovers, R.C., van Bergen en Henegouwen, P.M., Wilson, B.S., Lidke, D.S.: ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding. Nat. Struct. Mol. Biol. 18, 1244–1249 (2011)
Dawson, J.P., Bu, Z., Lemmon, M.A.: Ligand-induced structural transitions in ErbB receptor extracellular domains. Structure 15, 942–954 (2007)
Huxford, T., Mishler, D., Phelps, C.B., Huang, D.B., Sengchanthalangsy, L.L., Reeves, R., Hughes, C.A., Komives, E.A., Ghosh, G.: Solvent exposed non-contacting amino acids play a critical role in NF-κB/IκBα complex formation. J. Mol. Biol. 324, 587–597 (2002)
Mandell, J.G., Baerga-Ortiz, A., Akashi, S., Takio, K., Komives, E.A.: Solvent accessibility of the thrombin-thrombomodulin interface. J. Mol. Biol. 306, 575–589 (2001)
Dharmasiri, K., Smith, D.L.: Mass spectrometric determination of isotopic exchange rates of amide hydrogens located on the surfaces of proteins. Anal. Chem. 68, 2340–2344 (1996)
Engen, J.R.: Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS. Anal. Chem. 81, 7870–7875 (2009)
Zhang, Z., Smith, D.L.: Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 2, 522–531 (1993)
Smith, D.L.: Local structure and dynamics in proteins characterized by hydrogen exchange and mass spectrometry. Biochemistry (Mosc.) 63, 285–293 (1998)
Rand, K.D., Zehl, M., Jensen, O.N., Jorgensen, T.J.: Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal. Chem. 81, 5577–5584 (2009)
Roepstorff, P., Fohlman, J.: Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11, 601 (1984)
Syka, J.E., Coon, J.J., Schroeder, M.J., Shabanowitz, J., Hunt, D.F.: Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 101, 9528–9533 (2004)
Ladner, R.C.: Mapping the epitopes of antibodies. Biotechnol. Genet. Eng. Rev. 24, 1–30 (2007)
Hager-Braun, C., Tomer, K.B.: Determination of protein-derived epitopes by mass spectrometry. Expert Rev. Proteomics 2, 745–756 (2005)
Clementi, N., Mancini, N., Castelli, M., Clementi, M., Burioni, R.: Characterization of epitopes recognized by monoclonal antibodies: experimental approaches supported by freely accessible bioinformatic tools. Drug Discov. Today 18, 464–474 (2013)
Ahn, J., Engen, J.R.: The use of hydrogen/deuterium exchange mass spectrometry in epitope mapping. Chem. Today 31, 25–28 (2013)
Acknowledgments
The authors thank Professor Thomas E. Wales for helpful discussions. The authors also thank Dr. Bruce Car, Dr. Morrey Atkinson, and Dr. Peter Moesta from Bristol-Myers Squibb Company for their support of this project. This work was supported in part by grants from the National Institute of Health (GM086507 and GM 101135) and a research collaboration with the Waters Corporation.
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Iacob, R.E., Chen, G., Ahn, J. et al. The Influence of Adnectin Binding on the Extracellular Domain of Epidermal Growth Factor Receptor. J. Am. Soc. Mass Spectrom. 25, 2093–2102 (2014). https://doi.org/10.1007/s13361-014-0973-1
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DOI: https://doi.org/10.1007/s13361-014-0973-1