The kinetics of the hydrogen/deuterium exchange of epidermal growth factor receptor ligands

Biophysical Journal

Volumn 94, Issue 10, 2008, Pages 4041-4055

  Iloro, Ibon ^a   Narváez, Daniel ^a   Guillén, Nancy ^a   Camacho, Carlos M ^a   Guillén, Lalisse ^a   Cora, Elsa ^a,b   Pastrana Ríos, Belinda ^a  

^a UNIVERSITY OF PUERTO RICO   (Puerto Rico)

^b UNIVERSITY OF PUERTO RICO   (Puerto Rico)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; LIGAND;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DEUTERIUM HYDROGEN EXCHANGE; KINETICS; METHODOLOGY; PROTEIN CONFORMATION; ULTRASTRUCTURE;

COMPUTER SIMULATION; DEUTERIUM EXCHANGE MEASUREMENT; KINETICS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; RECEPTOR, EPIDERMAL GROWTH FACTOR;

EID: 43849098614     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.125856     Document Type: Article

References (60)

1. Riese, D. J., and D. F. Stern. 1998. Specificity within the EGF family/ErbB receptor family signaling network. Bioessays. 20:41-18.
2. Klein, P., D. Mattoon, M. A. Lemmon, and J. Schlessinger. 2004. A structure-based model for ligand binding and dimerization of EGF receptors. Proc. Natl. Acad. Sci. USA. 101:929-934.
3. Garrett, T. P., N. M. Mckern, M. Lou, T. C. Elleman, T. E. Adams, G.O. Lovrecz, H. J. Zhu, F. Walker, M. J. Frenkel, P. A. Hoyne, R. N. Jorissen, E. C. Nice, A. W. Burgess, and C. W. Ward. 2002. Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor α. Cell. 110:763-773.
4. Ogiso, H., R. Ishitani, O. Nureki, S. Fukai, M. Yamanaka, J. H. Kim, K. Saito, A. Sakamoto, M. Inoue, M. Shirouzu, and S. Yokoyama. 2002. Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell. 110:775-787.
5. Burgess, A. W., H. S. Cho, C. Eigenbrot, K. M. Ferguson, T. P. Garrett, D. J. Leahy, M. A. Lemmon, M. X. Sliwkowski, C. W. Ward, and S. Yokoyama. 2003. An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol. Cell. 12:541-552.
6. Lenferink, A. E., E. J. van Zoelen, M. J. van Vugt, S. Grothe, W. van Rotterdam, M. L. van De Poll, and M. D. O'Connor-McCourt. 2000. Superagonist activation of ErbB-1 by EGF-related growth factors with enhanced association and dissociation rate constants. J. Biol. Chem. 275:26748-26753.
7. Davis-Fleischer, K. M., and G. E. Besner. 1998. Structure and function of heparin-binding EGF-like growth factor (HB-EGF). Front. Biosci. 3:d288-d299.
8. Freimann, S., I. Ben-Ami, A. Dantes, R. Ron-El, and A. Amsterdam. 2004. EGF-like factor epiregulin and amphiregulin expression is regulated by gonadotropins/cAMP in human ovarian follicular cells. Biochem. Biophys. Res. Commun. 324:829-834.
9. Higashiyama, S., K. Lau, G. E. Besner, J. A. Abraham, and M. Klagsbrun. 1992. Structure of heparin-binding EGF-like growth factor. Multiple forms, primary structure, and glycosylation of the mature protein. J. Biol. Chem. 267:6205-6212.
10. Shoyab, M., G. D. Plowman, V. L. McDonald, J. G. Bradley, and G. J. Todaro. 1989. Structure and function of human amphiregulin: a member of the epidermal growth factor family. Science. 243:1074-1076.
11. Louie, G. V., W. Yang, M. E. Bowman, and S. Choe. 1997. Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor. Mol. Cell. 1:67-78.
12. Montelione, G. T., K. Wuthrich, A. W. Burgess, E. C. Nice, G. Wagner, K. D. Gibson, and H. A. Scheraga. 1992. Solution structure of murine epidermal growth-factor determined by NMR-spectroscopy and refined by energy minimization with restraints. Biochemistry. 31:236-249.
13. Thorne, B. A., and G. D. Plowman. 1994. The heparin-binding domain of amphiregulin necessitates the precursor pro-region for growth factor secretion. Mol. Cell. 1:67-78.
14. Sato, K., T. Nakamura, M. Mizuguchi, K. Miura, M. Tada, T. Aizawa, T. Gomi, K. Miyamoto, and K. Kawano. 2003. Solution structure of epiregulin and the effect of its C-terminal domain for receptor binding affinity. FEBS Lett. 553:232-238.
15. Baba, I., S. Shirasawa, R. Iwamoto, K. Okumura, T. Tsunoda, M. Nishioka, K. Fukuyama, K. Yamamoto, E. Mekada, and T. Sasazuki. 2000. Involvement of deregulated epiregulin expression in tumorigenesis in vivo through activated Ki-Ras signaling pathway in human colon cancer cells. Cancer Res. 60:6886-6889.
16. Torring, N., F. D. Hansen, B. S. Sorensen, T. F. Orntoft, and E. Nexo. 2005. Increase in amphiregulin and epiregulin in prostate cancer xenograft after androgen deprivation-impact of specific HER1 inhibition. Prostate. 64:1-8.
17. Jones, J. T., R. W. Akita, and M. X. Sliwkowski. 1999. Binding specificities and affinities of egf domains for ErbB receptors. FEBS Lett. 447:227-231.
18. Derynck, R. R., M. E. Winkler, E. Y. Chen, and D. V. Goeddel. 2005. Human transforming growth factor-α: precursor structure and expression in E. coli. Cell. 38:287-297.
19. Alwan, H. A.,E. J. van Zoelen, and J. E. M. van Leeuwen. 2003. Ligandinduced lysosomal epidermal growth factor receptor (EGFR) degradation is preceded by proteosome-dependent EGFR de-ubiquitination. J. Biol. Chem. 278:35781-35790.
20. Groenen, L. C., E. C. Nice, and A. W. Burgess. 1994. Structure-function relationships for the EGF/TGF-α family of mitogens. Growth Factors. 11:235-257.
21. Carpenter, G., and S. Cohen. 1990. Epidermal growth-factor. J. Biol. Chem. 265:7709-7712.
22. Kohda, D., N. Go, K. Hayashi, and F. Inagaki. 1988. Tertiary structure of mouse epidermal growth factor determined by two-dimensional 1H NMR. J. Biochem. (Tokyo). 103:741-743.
23. Kohda, D., C. Kodama, R. Kase, H. Nomoto, K. Hayashi, and F. Inagaki. 1988. A comparative 1H NMR study of mouse α (1-53) and β (2-53) epidermal growth factors. Biochem. Int. 16:647-654.
24. Kohda, D., and F. Inagaki. 1988. Complete sequence specific 1H NMR resonance assignments for mouse epidermal growth factor. J. Biochem. (Tokyo). 103:554-571.
25. Montelione, G. T., M. E. Winkler, L. E. Burton, E. Rinderknecht, M. B. Sporn, and G. Wagner. 1989. Sequence-specific 1H-NMR assignments and identification of two small antiparallel β-sheets in the solution structure of recombinant human transforming growth factor a. Proc. Natl. Acad. Sci. USA. 86:1519-1523.
26. Kline,T.P.,F.K.Brown,S.C.Brown,P.W.Jeffs,K.D.Kopple, and L. Mueller. 1990. Solution structures of human transforming growth factor-α derived from H-1-NMR data. Biochemistry. 29: 7805-7813.
27. Harvey, T. S., A. J. Wilkinson, M. J. Tappin, R. M. Cooke, and I. D. Campbell. 1991. The solution structure of human transforming growth factor-a. Eur. J. Biochem. 198:555-562.
28. Kohda, D., T. Sawada, and F. Inagaki. 1991. Characterization of pH titration shifts for all the nonlabile proton resonances in a protein by two-dimensional NMR: the case of mouse epidermal growth factor. Biochemistry. 30:4896-4900.
29. Kohda, D., and F. Inagaki. 1992. 3-Dimensional nuclear-magnetic-resonance structures of mouse epidermal growth-factor in acidic and physiological pH solutions. Biochemistry. 31:11928-11939.
30. Moy, F. J., Y. C. Li, P. Rauenbuehler, M. E. Winkler, H. A. Scheraga, and G. T. Montelione. 1993. Solution structure of human type-α transforming growth-factor determined by heteronuclear NMR-spectroscopy and refined by energy minimization with restraints. Biochemistry. 32: 7334-7353.
31. Li, Y. C., and G. T. Montelione. 1995. Human type-α transforming growth-factor undergoes slow conformational exchange between multiple backbone conformations as characterized by N-15 relaxation measurements. Biochemistry. 34:2408-2423.
32. Fadel, A. R., D. Q. Jin, G. T. Montelione, and R. M. Levy. 1995. Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type α transforming growth factor. J. Biomol. NMR. 6:221-226.
33. Stein, R. A., and J. V. Staros. 2000. Evolutionary analysis of the ErbB receptor and ligand families. J. Mol. Evol. 50:397-412.
34. Kabsch, W., and C. Sanders. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
35. Chang, J.-Y., and L. Li. 2002. The disulfide structure of denatured epidermal growth factor: preparation of scrambled disulfide isomers. J. Protein Chem. 21:203-213.
36. DeWitt, A., T. Iida, H. Y. Lam, V. Hill, H. S. Wiley, and D. A. Lauffenburger. 2002. Affinity regulates spatial range of EGF receptor autocrine ligand binding. Dev. Biol. 250:305-316.
37. Neelam, B., A. Richter, S. G. Chamberlin, S. M. Puddicombe, L. Wood, M. B. Murrray, K. Nandagopal, S. K. Niyogi, and D. Davies. 1998. Structure-function studies of ligand-induced epidermal growth factor receptor dimerization. Biochemistry. 37:4884-4891.
38. Wigens, M., T. Wama, H. van Ingen, C. Stortelers, J. E. M. van Leeuwen, E. J. van Zoelen, and G. W. Vuister. 2003. Structural analysis of an epidermal growth factor/transforming growth factor-α chimera with unique ErbB binding specificity. J. Biol. Chem. 278: 39114-39123.
39. Holladay, L. A., C. R. Savage, S. Cohen, and D. Puett. 1976. Conformation and unfolding thermodynamics of epidermal growth and derivatives. Biochemistry. 15:2624-2633.
40. Acha, V., J. M. Ruysschaert, and E. Goormaghtigh. 2001. Stacks of close to 100 phospholipid bilayers fully accessible to proteins-an ATR-FTIR-based chemometric analysis on hydrated phospholipid films. Anal. Chim. Acta. 435:215-226.
41. Goormaghtigh, E., H. H. J. deJongh, and J. M. Ruysschaert. 1996. Relevance of protein thin films prepared for attenuated total reflection Fourier transform infrared spectroscopy: significance of the pH. Appl. Spectrosc. 50:1519-1527.
42. Ortiz,M.,Z.Sanoguet,H. Hu,W.J.Chazin,C.McMurray,J.L. Salisbury, and B. Pastrana-Rios. 2005. Dynamics of hydrogen-deuterium exchange in Chlamydomonas centrin. Biochemistry. 44: 2409-2418.
43. Raussens, V., J. M. Ruysschaert, and E. Goormaghtigh. 2004. Analysis of 1H/2H exchange kinetics using model infrared spectra. Appl. Spectrosc. 58:68-82.
44. Vigano, C., M. Smeyers, V. Raussens, F. Scheirlinckx, J. M. Ruysschaert, and E. Goormaghtigh. 2004. Hydrogen-deuterium exchange in membrane proteins monitored by IR spectroscopy: a new tool to resolve protein structure and dynamics. Biopolymers. 74:19-26.
45. Arrondo, J. L. R., A. Muga, J. Castresana, and F. M. Goni. 1993. Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy. Prog. Biophys. Mol. Biol. 59:23-56.
46. Goormaghtigh, E., V. Raussens, and J. M. Ruysschaert. 1999. Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. Biochim. Biophys. Acta. 1422:105-185.
47. Nabet, A., and M. Pézolet. 1997. Two-dimensional FT-IR spectroscopy: a powerful method to study the secondary structure of proteins using H-D exchange. Appl. Spectrosc. 51:466-469.
48. Graff, D. K., B. Pastrana-Rios, S. Y. Venyaminov, and F. G. Prendergast. 1997. The effects of chain length and thermal denaturation on helix-forming peptides: a mode-specific analysis using 2D FT-IR. J. Am. Chem. Soc. 119:11282-11294.
49. Krimm, S., and J. Bandekar. 1986. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv. Protein Chem. 38:181-364.
50. Arrondo, J. L., and F. M. Goni. 1999. Structure and dynamics of membrane proteins as studied by infrared spectroscopy. Prog. Biophys. Mol. Biol. 72:367-405.
51. Pastrana-Rios, B. 2001. Mechanism of unfolding of a model helical peptide. Biochemistry. 40:9074-9081.
52. Pastrana-Rios, B., W. Ocana, M. Rios, G. L. Vargas, G. Ysa, G. Poynter, J. Tapia, and J. L. Salisbury. 2002. Centrin: its secondary structure in the presence and absence of cations. Biochemistry. 41:6911-6919.
53. Chirgadze, Y. N., O. V. Fedorov, and N. P. Trushina. 1975. Estimation of amino acid residue side-chain absorption in the infrared spectra of protein solutions in heavy water. Biopolymers. 14:679-694.
54. 2O) solutions. 1. Spectral parameters of amino-acid residue absorption-bands. Biopolymers. 30: 1243-1257.
55. 2O) solutions. 2. Amide absorption-bands of polypeptides and fibrous proteins in α-coil, β-coil, and random coil conformations. Biopolymers. 30:1259-1271.
56. Meskers, S., J. M. Ruysschaert, and E. Goormaghtigh. 1999. Hydrogen-deuterium exchange of streptavidin and its complex with biotin studied by 2D-attenuated total reflection Fourier transform infrared spectroscopy. J. Am. Chem. Soc. 121:5115-5122.
57. Noda, I., A. E. Dowrey, C. Marcott, G. M. Story, and Y. Ozaki. 2000. Generalized two-dimensional correlation spectroscopy. Appl. Spec-trosc. 54:236A-248A.
58. Ferguson, K. M., M. B. Berger, J. M. Mendrola, C. Hyun-Soo, D. J. Leahy, and M. A. Lemmon. 2003. EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization. Mol. Cell. 11:507-517.
59. ExPASy - UniProt Knowledgebase. 2007. Swiss-Prot and TrEMBL. http://expasy.org/sprot/.
60. Kyte, J., and R. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.