Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers

Biochimica et Biophysica Acta - General Subjects

Volumn 1820, Issue 12, 2012, Pages 1908-1914

  Arai, Hiromi ^a   Glabe, Charles ^a   Luecke, Hartmut ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Irvine   (United States)

Author keywords

Amyloid; IgG; Immunoglobulin; Oligomer; Rabbit

Indexed keywords

AMYLOID PROTEIN; IMMUNOGLOBULIN FC FRAGMENT; IMMUNOGLOBULIN FRAGMENT; IMMUNOGLOBULIN G; OLIGOMER;

ANTIGEN ANTIBODY COMPLEX; ANTIGEN RECOGNITION; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DISULFIDE BOND; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; X RAY CRYSTALLOGRAPHY;

AMYLOID; ANIMALS; ANTIBODIES, MONOCLONAL; BINDING SITES, ANTIBODY; CELLS, CULTURED; CRYSTALLOGRAPHY, X-RAY; DISULFIDES; HUMANS; IMMUNOGLOBULIN FAB FRAGMENTS; KIDNEY; MODELS, MOLECULAR; PROTEIN CONFORMATION; RABBITS;

ORYCTOLAGUS CUNICULUS;

EID: 84866649947     PISSN: 03044165     EISSN: 18728006     Source Type: Journal    
DOI: 10.1016/j.bbagen.2012.08.016     Document Type: Article

References (38)

1. C.G. Glabe Structural classification of toxic amyloid oligomers J. Biol. Chem. 283 2008 29639 29643
2. C. Haass, and D.J. Selkoe Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid beta-peptide Nat. Rev. Mol. Cell Biol. 8 2007 101 112
3. M. Margittai, and R. Langen Fibrils with parallel in-register structure constitute a major class of amyloid fibrils: molecular insights from electron paramagnetic resonance spectroscopy Q. Rev. Biophys. 41 2008 265 297
4. R. Tycko Molecular structure of amyloid fibrils: insights from solid-state NMR Q. Rev. Biophys. 39 2006 1 55
5. M.R. Sawaya, S. Sambashivan, R. Nelson, M.I. Ivanova, S.A. Sievers, M.I. Apostol, M.J. Thompson, M. Balbirnie, J.J. Wiltzius, H.T. McFarlane, A.O. Madsen, C. Riekel, and D. Eisenberg Atomic structures of amyloid cross-beta spines reveal varied steric zippers Nature 447 2007 453 457
6. R. Kayed, E. Head, F. Sarsoza, T. Saing, C.W. Cotman, M. Necula, L. Margol, J. Wu, L. Breydo, J.L. Thompson, S. Rasool, T. Gurlo, P. Butler, and C.G. Glabe Fibril specific, conformation dependent antibodies recognize a generic epitope common to amyloid fibrils and fibrillar oligomers that is absent in prefibrillar oligomers Mol. Neurodegener. 2 2007 18
7. J.W. Wu, L. Breydo, J.M. Isas, J. Lee, Y.G. Kuznetsov, R. Langen, and C. Glabe Fibrillar oligomers nucleate the oligomerization of monomeric amyloid {beta} but do not seed fibril formation J. Biol. Chem. 285 2010 6071 6079
8. R. Kayed, A. Pensalfini, L. Margol, Y. Sokolov, F. Sarsoza, E. Head, J. Hall, and C. Glabe Annular protofibrils are a structurally and functionally distinct type of amyloid oligomer J. Biol. Chem. 284 2009 4230 4237
9. E. Cerf, R. Sarroukh, S. Tamamizu-Kato, L. Breydo, S. Derclaye, Y.F. Dufrene, V. Narayanaswami, E. Goormaghtigh, J.M. Ruysschaert, and V. Raussens Antiparallel beta-sheet: a signature structure of the oligomeric amyloid beta-peptide Biochem. J. 421 2009 415 423
10. M. Cheon, I. Chang, S. Mohanty, L.M. Luheshi, C.M. Dobson, M. Vendruscolo, and G. Favrin Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils PLoS Comput. Biol. 3 2007 1727 1738
11. R. Kayed, E. Head, J.L. Thompson, T.M. McIntire, S.C. Milton, C.W. Cotman, and C.G. Glabe Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis Science 300 2003 486 489
12. R. Kayed, I. Canto, L. Breydo, S. Rasool, T. Lukacsovich, J. Wu, R. Albay 3rd, A. Pensalfini, S. Yeung, E. Head, J.L. Marsh, and C. Glabe Conformation dependent monoclonal antibodies distinguish different replicating strains or conformers of prefibrillar abeta oligomers Mol. Neurodegener. 5 2010 57
13. E. Girardi, M.D. Holdom, A.M. Davies, B.J. Sutton, and A.J. Beavil The crystal structure of rabbit IgG-Fc Biochem. J. 417 2009 77 83
14. R.S. Nezlin The Immunoglobulins: Structure and Function 1998 Academic Press San Diego
15. C.A. Clarkson, D. Beale, J.W. Coadwell, and D.B. Symons Sequence of ovine Ig gamma 2 constant region heavy chain cDNA and molecular modelling of ruminant IgG isotypes Mol. Immunol. 30 1993 1195 1204
16. J. Rejnek, E. Appella, R.G. Mage, and R.A. Reisfeld Subtypes of rabbit kappa light polypeptide chains associated with the beta locus Biochemistry 8 1969 2712 2718
17. M. Popkov, R.G. Mage, C.B. Alexander, S. Thundivalappil, C.F. Barbas III, and C. Rader Rabbit immune repertoires as sources for therapeutic monoclonal antibodies: the impact of kappa allotype-correlated variation in cysteine content on antibody libraries selected by phage display J. Mol. Biol. 325 2003 325 335
18. A.D. Strosberg, M.N. Margolies, and E. Haber The interdomain disulfide bond of a homogeneous rabbit pneumococcal antibody light chain J. Immunol. 115 1975 1422 1424
19. R.J. Poljak, L.M. Amzel, H.P. Avey, B.L. Chen, R.P. Phizackerley, and F. Saul Three-dimensional structure of the Fab′ fragment of a human immunoglobulin at 2,8-A resolution Proc. Natl. Acad. Sci. U. S. A. 70 1973 3305 3310
20. R.L. Stanfield, A. Zemla, I.A. Wilson, and B. Rupp Antibody elbow angles are influenced by their light chain class J. Mol. Biol. 357 2006 1566 1574
21. M.A. DiMattia, N.R. Watts, S.J. Stahl, C. Rader, P.T. Wingfield, D.I. Stuart, A.C. Steven, and J.M. Grimes Implications of the HIV-1 Rev dimer structure at 3.2 A resolution for multimeric binding to the Rev response element Proc. Natl. Acad. Sci. U. S. A. 107 2010 5810 5814
22. I.J. O'Donnell, B. Frangione, and R.R. Porter The disulphide bonds of the heavy chain of rabbit immunoglobulin G Biochem. J. 116 1970 261 268
23. C. Haupt, I. Morgado, S.T. Kumar, C. Parthier, M. Bereza, P. Hortschansky, M.T. Stubbs, U. Horn, and M. Fandrich Amyloid fibril recognition with the conformational B10 antibody fragment depends on electrostatic interactions J. Mol. Biol. 405 2011 341 348
24. Z.F. Kanyo, K.M. Pan, R.A. Williamson, D.R. Burton, S.B. Prusiner, R.J. Fletterick, and F.E. Cohen Antibody binding defines a structure for an epitope that participates in the PrPC->PrPSc conformational change J. Mol. Biol. 293 1999 855 863
25. H. Remaut, and G. Waksman Protein-protein interaction through beta-strand addition Trends Biochem. Sci. 31 2006 436 444
26. Y. Yoshiike, R. Minai, Y. Matsuo, Y.R. Chen, T. Kimura, and A. Takashima Amyloid oligomer conformation in a group of natively folded proteins PLoS One 3 2008 e3235
27. J.M. Perchiacca, A.R. Ladiwala, M. Bhattacharya, and P.M. Tessier Structure-based design of conformation- and sequence-specific antibodies against amyloid beta Proc. Natl. Acad. Sci. U. S. A. 109 2012 84 89
28. D.C. Ekiert, R.H. Friesen, G. Bhabha, T. Kwaks, M. Jongeneelen, W. Yu, C. Ophorst, F. Cox, H.J. Korse, B. Brandenburg, R. Vogels, J.P. Brakenhoff, R. Kompier, M.H. Koldijk, L.A. Cornelissen, L.L. Poon, M. Peiris, W. Koudstaal, I.A. Wilson, and J. Goudsmit A highly conserved neutralizing epitope on group 2 infuenza A viruses Science 2011 843 850
29. J.W. Pflugrath The finer things in X-ray diffraction data collection Acta Crystallogr. D: Biol. Crystallogr. 55 1999 1718 1725
30. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674
31. E. Potterton, P. Briggs, M. Turkenburg, and E. Dodson A graphical user interface to the CCP4 program suite Acta Crystallogr. D: Biol. Crystallogr. 59 2003 1131 1137
32. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. D: Biol. Crystallogr. 53 1997 240 255
33. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D: Biol. Crystallogr. 60 2004 2126 2132
34. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, and G.L. Warren Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr. D: Biol. Crystallogr. 54 1998 905 921
35. A.T. Brunger Version 1.2 of the crystallography and NMR system Nat. Protoc. 2 2007 2728 2733
36. R.A. Laskowski, M.W. Macarthur, D.S. Moss, and J.M. Thornton Procheck - a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
37. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38
38. N.A. Baker, D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl. Acad. Sci. U. S. A. 98 2001 10037 10041