A regulatable switch mediates self-association in an immunoglobulin fold

Nature Structural and Molecular Biology

Volumn 15, Issue 9, 2008, Pages 965-971

  Calabrese, Matthew F ^a   Eakin, Catherine M ^a   Wang, Jimin M ^a   Miranker, Andrew D ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA 2 MICROGLOBULIN; COPPER; HEXACHLOROPHENE; PROLINE;

ARTICLE; CONTROLLED STUDY; HYDROPHOBICITY; ISOMERIZATION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

AMYLOID; AMYLOIDOSIS; BETA 2-MICROGLOBULIN; COPPER; CRYSTALLOGRAPHY, X-RAY; ELECTRON SPIN RESONANCE SPECTROSCOPY; HUMANS; HYDROPHOBICITY; IMMUNOGLOBULINS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN FOLDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, QUATERNARY; RENAL DIALYSIS;

EID: 51349128031     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.1483     Document Type: Article

References (57)

1. Burgess, A.W. et al. An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol. Cell 12, 541-552 (2003).
2. Pollard, T.D. & Borisy, G.G. Cellular motility driven by assembly and disassembly of actin filaments. Cell 112, 453-465 (2003).
3. Egelman, E.H. & Orlova, A. Allostery, cooperativity, and different structural states in F-actin. J. Struct. Biol. 115, 159-162 (1995).
4. Frederick, K.B., Sept, D. & De La Cruz, E.M. Effects of solution crowding on actin polymerization reveal the energetic basis for nucleotide-dependent filament stability. J. Mol. Biol. 378, 540-550 (2008).
5. Sunshine, H.R., Hofrichter, J., Ferrone, F.A. & Eaton, W.A. Oxygen binding by sickle cell hemoglobin polymers. J. Mol. Biol. 158, 251-273 (1982).
6. Rochet, J.C. & Lansbury, P.T., Jr. Amyloid fibrillogenesis: themes and variations. Curr. Opin. Struct. Biol. 10, 60-68 (2000).
7. Chiti, F. & Dobson, C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75, 333-366 (2006).
8. Santos, M. et al. Defective iron homeostasis in beta 2-microglobulin knockout mice recapitulates hereditary hemochromatosis in man. J. Exp. Med. 184, 1975-1985 (1996).
9. 2-microglobulin knockout mice are highly susceptible to polyoma virus tumorigenesis. Virology 252, 275-284 (1998).
10. 2-microglobulin trapped by non-native prolyl peptide bond. J. Mol. Biol. 348, 383-397 (2005).
11. Jahn, T.R., Parker, M.J., Homans, S.W. & Radford, S.E. Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nat. Struct. Mol. Biol. 13, 195-201 (2006).
12. Chiti, F. et al. Detection of two partially structured species in the folding process of the amyloidogenic protein β2-microglobulin. J. Mol. Biol. 307, 379-391 (2001).
13. Eakin, C.M., Attenello, F.J., Morgan, C.J. & Miranker, A.D. Oligomeric assembly of native-like precursors precedes amyloid formation by β2 microglobulin. Biochemistry 43, 7808-7815 (2004).
14. Okon, M., Bray, P. & Vucelic, D. 1H NMR assignments and secondary structure of human β2-microglobulin in solution. Biochemistry 31, 8906-8915 (1992).
15. Morgan, C.J., Gelfand, M., Atreya, C. & Miranker, A.D. Kidney dialysis-associated amyloidosis: a molecular role for copper in fiber formation. J. Mol. Biol. 309, 339-345 (2001).
16. Floege, J. & Ehlerding, G. β2-microglobulin-associated amyloidosis. Nephron 72, 9-26 (1996).
17. Menaa, C., Esser, E. & Sprague, S.M. β2-microglobulin stimulates osteoclast formation. Kidney Int. 73, 1275-1281 (2008).
18. 2-microglobulin-related amyloid fibrils at a neutral pH. Biochemistry 43, 11075-11082 (2004).
19. Yamamoto, S. et al. Glycosaminoglycans enhance the trifluoroethanol-induced extension of β2-microglobulin-related amyloid fibrils at a neutral pH. J. Am. Soc. Nephrol. 15, 126-133 (2004).
20. 2-microglobulin and amyloid formation in vitro. Biochemistry 39, 8735-8746 (2000).
21. Esposito, G. et al. Removal of the N-terminal hexapeptide fromhuman β2-microglobulin facilitates protein aggregation and fibril formation. Protein Sci. 9, 831-845 (2000).
22. 2-microglobulin and hen egg-white lysozyme into amyloid fibrils. J. Mol. Biol. 372, 981-991 (2007).
23. 2-microglobulin amyloid formation at neutral pH. Biochemistry 45, 2311-2321 (2006).
24. Linse, S. et al. Nucleation of protein fibrillation by nanoparticles. Proc. Natl. Acad. Sci. USA 104, 8691-8696 (2007).
25. Eakin, C.M., Berman, A.J. & Miranker, A.D. A native to amyloidogenic transition regulated by a backbone trigger. Nat. Struct. Mol. Biol. 13, 202-208 (2006).
26. Dobson, C.M. An accidental breach of a protein's natural defenses. Nat. Struct. Mol. Biol. 13, 295-297 (2006).
27. Smith, A.M., Jahn, T.R., Ashcroft, A.E. & Radford, S.E. Direct observation of oligomeric species formed in the early stages of amyloid fibril formation using electrospray ionisation mass spectrometry. J. Mol. Biol. 364, 9-19 (2006).
28. Calabrese, M.F. & Miranker, A.D. Formation of a stable oligomer of β2 microglobulin requires only transient encounter with Cu(II). J. Mol. Biol. 367, 1-7 (2007).
29. 2-microglobulin oligomers but is released upon amyloid formation. Protein Sci. 17, 748-759 (2008).
30. 2-microglobulin. Biochemistry 41, 10646-10656 (2002).
31. Verdone, G. et al. The solution structure of human β2-microglobulin reveals the prodromes of its amyloid transition. Protein Sci. 11, 487-499 (2002).
32. Cole, J.L. Analysis of heterogeneous interactions. Methods Enzymol. 384, 212-232 (2004).
33. Bjorkman, P.J. et al. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329, 506-512 (1987).
34. Richardson, J.S. & Richardson, D.C. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl. Acad. Sci. USA 99, 2754-2759 (2002).
35. 2-microglobulin reveals clues to its amyloidogenic properties. Proc. Natl. Acad. Sci. USA 99, 9771-9776 (2002).
36. 2-microglobulin formed at pH 7.0. J. Biochem. 142, 413-419 (2007).
37. 2-microglobulin H31Y variant 3D structure highlights the protein natural propensity towards intermolecular aggregation. J. Mol. Biol. 335, 1051-1064 (2004).
38. 2-microglobulin. Anal. Chem. 76, 3498-3504 (2004).
39. 2-microglobulin important for nucleation and elongation of aggregation. J. Mol. Biol. 378, 251-263 (2008).
40. Dobson, C.M. Protein folding and misfolding. Nature 426, 884-890 (2003).
41. 2-microglobulin fragment probed by solid-state NMR. Proc. Natl. Acad. Sci. USA 103, 18119-18124 (2006).
42. 2-microglobulin in amyloid formation at neutral pH. J. Mol. Biol. 330, 935-941 (2003).
43. 2- microglobulin. Nat. Struct. Biol. 9, 326-331 (2002).
44. 2- microglobulin amyloid fibril by H/D exchange. Nat. Struct. Biol. 9, 332-336 (2002).
45. 2- microglobulin amyloid fibrils. J. Biol. Chem. 283, 17279-17286 (2008).
46. Ramachander, R. & Bowie, J.U. SAM domains can utilize similar surfaces for the formation of polymers and closed oligomers. J. Mol. Biol. 342, 1353-1358 (2004).
47. 2-microglobulin suggests a molecular model for the fibril. Proc. Natl. Acad. Sci. USA 101, 10584-10589 (2004).
48. Bennett, M.J., Schlunegger, M.P. & Eisenberg, D. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 4, 2455-2468 (1995).
49. Wright, C.F., Teichmann, S.A., Clarke, J. & Dobson, C.M. The importance of sequence diversity in the aggregation and evolution of proteins. Nature 438, 878-881 (2005).
50. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
51. Storoni, L.C., McCoy, A.J. & Read, R.J. Likelihood-enhanced fast rotation functions. Acta Crystallogr. D Biol. Crystallogr. 60, 432-438 (2004).
52. Terwilliger, T.C. Maximum-likelihood density modification. Acta Crystallogr. D Biol. Crystallogr. 56, 965-972 (2000).
53. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).
54. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 (2004).
55. Lovell, S.C. et al. Structure validation by Cα geometry: φ, ψ and Cψ deviation. Proteins 50, 437-450 (2003).
56. Laskowski, R., MacArthur, M., Moss, D. & Thornton, J. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).
57. Kleywegt, G.J. & Brunger, A.T. Checking your imagination: applications of the free R value. Structure 4, 897-904 (1996).