Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis

Structure

Volumn 14, Issue 3, 2006, Pages 401-414

  Sivasubramanian, Arvind ^a,d   Chao, Ginger ^b   Pressler, Heather M ^b   Wittrup, K Dane ^b   Gray, Jeffrey J ^a,c,d  

^a Johns Hopkins University   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

^d JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; MONOCLONAL ANTIBODY;

ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIMERIZATION; MUTAGENESIS; MUTATION; PRIORITY JOURNAL; STEREOSPECIFICITY;

ANTIBODIES, MONOCLONAL; ANTIBODIES, NEOPLASM; COMPUTATIONAL BIOLOGY; EPITOPE MAPPING; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MUTAGENESIS; PROTEIN BINDING; RECEPTOR, EPIDERMAL GROWTH FACTOR; REPRODUCIBILITY OF RESULTS;

EID: 33644839662     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2005.11.022     Document Type: Article

References (60)

1. B. Al-Lazikani, A.M. Lesk, and C. Chothia Standard conformations for the canonical structures of immunoglobulins J. Mol. Biol. 273 1997 927 948
2. P. Aloy, E. Querol, F.X. Aviles, and M.J.E. Sternberg Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking J. Mol. Biol. 311 2001 395 408
3. A. Berchanski, B. Shapira, and M. Eisenstein Hydrophobic complementarity in protein-protein docking Proteins 56 2004 130 142
4. M.E. Bose, K.H. McConnell, K.A. Gardner-Aukema, U. Muller, M. Weinreich, J.L. Keck, and C.A. Fox The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain Mol. Cell. Biol. 24 2004 774 786
5. L. Bracci, A. Pini, A. Bernini, B. Lelli, C. Ricci, M. Scarselli, N. Niccolai, and P. Neri Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and α-bungarotoxin Biochem. J. 371 2003 423 427
6. C.J. Camacho, and D.W. Gatchell Successful discrimination of protein interactions Proteins 52 2003 92 97
7. G. Chao, J.R. Cochran, and K. Dane Wittrup Fine epitope mapping of anti-epidermal growth factor receptor antibodies through random mutagenesis and yeast surface display J. Mol. Biol. 342 2004 539 550
8. R. Chen, J. Mintseris, J. Janin, and Z.P. Weng A protein-protein docking benchmark Proteins 52 2003 88 91
9. H.S. Cho, K. Mason, K.X. Ramyar, A.M. Stanley, S.B. Gabelli, D.W. Denney, and D.J. Leahy Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab Nature 421 2003 756 760
10. C. Chothia, and A.M. Lesk Canonical structures for the hypervariable regions of immunoglobulins J. Mol. Biol. 196 1987 901 917
11. S.R. Comeau, D.W. Gatchell, S. Vajda, and C.J. Camacho ClusPro: a fully automated algorithm for protein-protein docking Nucleic Acids Res. 32 2004 W96 W99
12. M.D. Daily, D. Masica, A. Sivasubramanian, S. Somarouthu, and J.J. Gray CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock Proteins 60 2005 181 186
13. W.L. DeLano The PyMOL Molecular Graphics System 2002 DeLano Scientific San Carlos, CA
14. C. Dominguez, R. Boelens, and A.M. Bonvin HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
15. R.L. Dunbrack Jr., and F.E. Cohen Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 6 1997 1661 1681
16. N. Echols, D. Milburn, and M. Gerstein MolMovDB: analysis and visualization of conformational change and structural flexibility Nucleic Acids Res. 31 2003 478 482
17. K.M. Ferguson, M.B. Berger, J.M. Mendrola, H.S. Cho, D.J. Leahy, and M.A. Lemmon EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization Mol. Cell 11 2003 507 517
18. J. Fernandez-Recio, M. Totrov, and R. Abagyan ICM-DISCO docking by global energy optimization with fully flexible side-chains Proteins 52 2003 113 117
19. M.C. Franklin, K.D. Carey, F.F. Vajdos, D.J. Leahy, A.M. de Vos, and M.X. Sliwkowski Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex Cancer Cell 5 2004 317 328
20. K.A. Gardner, J. Rine, and C.A. Fox A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with the Orc1 protein in Saccharomyces cerevisiae Genetics 151 1999 31 44
21. T.P.J. Garrett, N.M. McKern, M.Z. Lou, T.C. Elleman, T.E. Adams, G.O. Lovrecz, H.J. Zhu, F. Walker, M.J. Frenkel, and P.A. Hoyne Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor alpha Cell 110 2002 763 773
22. J.J. Gray, S.E. Moughon, T. Kortemme, O. Schueler-Furman, K.M. Misura, A.V. Morozov, and D. Baker Protein-protein docking predictions for the CAPRI experiment Proteins 52 2003 118 122
23. J.J. Gray, S.E. Moughon, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl, and D. Baker Protein-protein docking with simultaneous optimization of rigid body displacement and side-chain conformations J. Mol. Biol. 331 2003 281 299
24. P.M. Harari Epidermal growth factor receptor inhibition strategies in oncology Endocr. Relat. Cancer 11 2004 689 708
25. P. Herzyk, and R.E. Hubbard Using experimental information to produce a model of the transmembrane domain of the ion channel phospholamban Biophys. J. 74 1998 1203 1214
26. Z. Hou, D.A. Bernstein, C.A. Fox, and J.L. Keck Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing Proc. Natl. Acad. Sci. USA 102 2005 8489 8494
27. S.J. Hubbard, and J.M. Thornton NACCESS 1993 Department of Biochemistry and Molecular Biology, Univ. College London
28. J. Janin Assessing predictions of protein-protein interaction: the CAPRI experiment Protein Sci. 14 2005 278 283
29. T.G. Johns, E. Stockert, G. Ritter, A.A. Jungbluth, H.J.S. Huang, W.K. Cavenee, F.E. Smyth, C.M. Hall, N. Watson, and E.C. Nice Novel monoclonal antibody specific for the DE2-7 epidermal growth factor receptor (EGFR) that also recognizes the EGFR expressed in cells containing amplification of the EGFR gene Int. J. Cancer 98 2002 398 408
30. T.G. Johns, T.E. Adams, J.R. Cochran, N.E. Hall, P.A. Hoyne, M.J. Olsen, Y.S. Kim, J. Rothacker, E.C. Nice, and F. Walker Identification of the epitope for the epidermal growth factor receptor-specific monoclonal antibody 806 reveals that it preferentially recognizes an untethered form of the receptor J. Biol. Chem. 279 2004 30375 30384
31. T.G. Johns, I. Mellman, G.A. Cartwright, G. Ritter, L.J. Old, A.W. Burgess, and A.M. Scott The antitumor monoclonal antibody 806 recognizes a high-mannose form of the EGF receptor that reaches the cell surface when cells over-express the receptor FASEB J. 19 2005 780 782
32. M.K. Kim, W. Li, B.A. Shapiro, and G.S. Chirikjian A comparison between elastic network interpolation and MD simulation of 16S ribosomal RNA J. Biomol. Struct. Dyn. 21 2003 395 405
33. T. Kortemme, and D. Baker A simple physical model for binding energy hot spots in protein-protein complexes Proc. Natl. Acad. Sci. USA 99 2002 14116 14121
34. T. Kortemme, A.V. Morozov, and D. Baker An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes J. Mol. Biol. 326 2003 1239 1259
35. T. Lazaridis, and M. Karplus Effective energy function for proteins in solution Proteins 35 1999 133 152
36. L. Li, R. Chen, and Z.P. Weng RDOCK: refinement of rigid-body protein docking predictions Proteins 53 2003 693 707
37. S. Li, K.R. Schmitz, P.D. Jeffrey, J.J. Wiltzius, P. Kussie, and K.M. Ferguson Structural basis for inhibition of the epidermal growth factor receptor by cetuximab Cancer Cell 7 2005 301 311
38. R.B. Luwor, T.G. Johns, C. Murone, H.J.S. Huang, W.K. Cavenee, G. Ritter, L.J. Old, A.W. Burgess, and A.M. Scott Monoclonal antibody 806 inhibits the growth of tumor xenografts expressing either the de2-7 or amplified epidermal growth factor receptor (EGFR) but not wild-type EGFR Cancer Res. 61 2001 5355 5361
39. J.G. Mandell, V.A. Roberts, M.E. Pique, V. Kotlovyi, J.C. Mitchell, E. Nelson, I. Tsigelny, and L.F. Ten Eyck Protein docking using continuum electrostatics and geometric fit Protein Eng. 14 2001 105 113
40. I. Massova, and P.A. Kollman Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies J. Am. Chem. Soc. 121 1999 8133 8143
41. R. Mendez, R. Leplae, L. De Maria, and S.J. Wodak Assessment of blind predictions of protein-protein interactions: current status of docking methods Proteins 52 2003 51 67
42. R. Mendez, R. Leplae, M.F. Lensink, and S.J. Wodak Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures Proteins 60 2005 150 169
43. K. Mishima, T.G. Johns, R.B. Luwor, A.M. Scott, E. Stockert, A.A. Jungbluth, X.D. Ji, P. Suvarna, J.R. Voland, and L.J. Old Growth suppression of intracranial xenografted glioblastomas overexpressing mutant epidermal growth factor receptors by systemic administration of monoclonal antibody (mAb) 806, a novel monoclonal antibody directed to the receptor Cancer Res. 61 2001 5349 5354
44. V. Nanda, and W.F. DeGrado Automated use of mutagenesis data in structure prediction Proteins 59 2005 454 466
45. B.V. Norledge, R.J. Petrovan, W. Ruf, and A.J. Olson The tissue factor/factor VIIa/factor Xa complex: a model built by docking and site-directed mutagenesis Proteins 53 2003 640 648
46. H. Ogiso, R. Ishitani, O. Nureki, S. Fukai, M. Yamanaka, J.H. Kim, K. Saito, A. Sakamoto, M. Inoue, M. Shirouzu, and S. Yokoyama Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains Cell 110 2002 775 787
47. Old, L.J., Johns, T.G., Panousis, C., Scott, A.M., Renner, C., Ritter, G., Jungbluth, A., Stockert, E., Collins, P., Cavanee, W.K., et al. (2002). PCT International Patent WO/02/092771.
48. R. Onrust, P. Herzmark, P. Chi, P.D. Garcia, O. Lichtarge, C. Kingsley, and H.R. Bourne Receptor and βγ binding sites in the α subunit of the retinal G protein transducin Science 275 1997 381 384
49. D.W. Ritchie, and G.J.L. Kemp Protein docking using spherical polar Fourier correlations Proteins 39 2000 178 194
50. D. Schneidman-Duhovny, Y. Inbar, V. Polak, M. Shatsky, I. Halperin, H. Benyamini, A. Barzilai, O. Dror, N. Haspel, R. Nussinov, and H.J. Wolfson Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking Proteins 52 2003 107 112
51. G.R. Smith, M.J.E. Sternberg, and P.A. Bates The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking J. Mol. Biol. 347 2005 1077 1101
52. S.S. Sridhar, L. Seymour, and F.A. Shepherd Inhibitors of epidermal-growth-factor receptors: a review of clinical research with a focus on non-small-cell lung cancer Lancet Oncol. 4 2003 397 406
53. S. Vajda, and C.J. Camacho Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol. 22 2004 110 116
54. A.D. van Dijk, R. Boelens, and A.M. Bonvin Data-driven docking for the study of biomolecular complexes FEBS J. 272 2005 293 312
55. F. Walker, S.G. Orchard, R.N. Jorissen, N.E. Hall, H.H. Zhang, P.A. Hoyne, T.E. Adams, T.G. Johns, C. Ward, and T.P.J. Garrett CR1/CR2 interactions modulate the functions of the cell surface epidermal growth factor receptor J. Biol. Chem. 279 2004 22387 22398
56. C. Wang, O. Schueler-Furman, and D. Baker Improved side-chain modeling for protein-protein docking Protein Sci. 14 2005 1328 1339
57. N.R. Whitelegg, and A.R. Rees WAM: an improved algorithm for modelling antibodies on the WEB Protein Eng. 13 2000 819 824
58. S.J. Wodak, and R. Mendez Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications Curr. Opin. Struct. Biol. 14 2004 242 249
59. Y. Yarden, and M.X. Sliwkowski Untangling the ErbB signalling network Nat. Rev. Mol. Cell Biol. 2 2001 127 137
60. M. Zacharias Protein-protein docking with a reduced protein model accounting for side-chain flexibility Protein Sci. 12 2003 1271 1282