Chain collapse of an amyloidogenic intrinsically disordered protein

Biophysical Journal

Volumn 101, Issue 7, 2011, Pages 1720-1729

  Jain, Neha ^a   Bhattacharya, Mily ^a   Mukhopadhyay, Samrat ^a  

^a INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH MOHALI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID PROTEIN; CASEIN; PEPTIDE; PYRENE; PYRENE DERIVATIVE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGY; CATTLE; CHEMISTRY; FLUORESCENCE POLARIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; LIGHT; METABOLISM; MOLECULAR GENETICS; PROTEIN MULTIMERIZATION; RADIATION SCATTERING;

AMINO ACID SEQUENCE; AMYLOIDOGENIC PROTEINS; ANIMALS; CASEINS; CATTLE; COMPUTATIONAL BIOLOGY; FLUORESCENCE POLARIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; LIGHT; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN MULTIMERIZATION; PYRENES; SCATTERING, RADIATION;

BOVINAE;

EID: 80053368232     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.08.024     Document Type: Article

References (52)

1. V.N. Uversky, and A.K. Dunker Understanding protein non-folding Biochim. Biophys. Acta 1804 2010 1231 1264
2. A.K. Dunker, and J.D. Lawson Z. Obradovic Intrinsically disordered protein J. Mol. Graph. Model. 19 2001 26 59 (Pubitemid 32411501)
3. P. Tompa Structure and Function of Intrinsically Disordered Proteins 2010 CRC Press Boca Raton, FL
4. V.N. Uversky Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding Protein J. 28 2009 305 325
5. P. Radivojac, and L.M. Iakoucheva A.K. Dunker Intrinsic disorder and functional proteomics Biophys. J. 92 2007 1439 1456 (Pubitemid 46393458)
6. H.J. Dyson, and P.E. Wright Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell Biol. 6 2005 197 208 (Pubitemid 40314921)
7. P. Tompa The interplay between structure and function in intrinsically unstructured proteins FEBS Lett. 579 2005 3346 3354 (Pubitemid 40804685)
8. A.K. Dunker, and I. Silman J.L. Sussman Function and structure of inherently disordered proteins Curr. Opin. Struct. Biol. 18 2008 756 764
9. H.J. Dyson, and P.E. Wright Unfolded proteins and protein folding studied by NMR Chem. Rev. 104 2004 3607 3622
10. M.M. Dedmon, and K. Lindorff-Larsen C.M. Dobson Mapping long-range interactions in α-synuclein using spin-label NMR and ensemble molecular dynamics simulations J. Am. Chem. Soc. 127 2005 476 477 (Pubitemid 40174345)
11. V.N. Uversky Natively unfolded proteins: a point where biology waits for physics Protein Sci. 11 2002 739 756 (Pubitemid 34241284)
12. E. Smyth, and C.D. Syme L.D. Barron Solution structure of native proteins with irregular folds from Raman optical activity Biopolymers 58 2001 138 151 (Pubitemid 32096458)
13. C.D. Syme, and E.W. Blanch L.D. Barron A Raman optical activity study of rheomorphism in caseins, synucleins and tau. New insight into the structure and behaviour of natively unfolded proteins Eur. J. Biochem. 269 2002 148 156 (Pubitemid 34107348)
14. S. Jeganathan, and M. von Bergen E. Mandelkow Global hairpin folding of tau in solution Biochemistry 45 2006 2283 2293 (Pubitemid 43271328)
15. G.R. Szilvay, and M.A. Blenner S. Banta A FRET-based method for probing the conformational behavior of an intrinsically disordered repeat domain from Bordetella pertussis adenylate cyclase Biochemistry 48 2009 11273 11282
16. A. Grupi, and E. Haas Segmental conformational disorder and dynamics in the intrinsically disordered protein α-synuclein and its chain length dependence J. Mol. Biol. 405 2011 1267 1283
17. S. Mukhopadhyay, and R. Krishnan A.A. Deniz A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures Proc. Natl. Acad. Sci. USA 104 2007 2649 2654 (Pubitemid 46327934)
18. A.C.M. Ferreon, and Y. Gambin A.A. Deniz Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence Proc. Natl. Acad. Sci. USA 106 2009 5645 5650
19. A.C.M. Ferreon, and C.R. Moran A.A. Deniz Single-molecule fluorescence studies of intrinsically disordered proteins Methods Enzymol. 472 2010 179 204
20. V.N. Uversky Amyloidogenesis of natively unfolded proteins Curr. Alzheimer Res. 5 2008 260 287 (Pubitemid 351850211)
21. K.K. Turoverov, I.M. Kuznetsova, and V.N. Uversky The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation Prog. Biophys. Mol. Biol. 102 2010 73 84
22. T. Scheibel, and S.L. Lindquist The role of conformational flexibility in prion propagation and maintenance for Sup35p Nat. Struct. Biol. 8 2001 958 962 (Pubitemid 33032364)
23. T.R. Serio, and A.G. Cashikar S.L. Lindquist Nucleated conformational conversion and the replication of conformational information by a prion determinant Science 289 2000 1317 1321 (Pubitemid 30656041)
24. D.M. Fowler, and A.V. Koulov J.W. Kelly Functional amyloid - from bacteria to humans Trends Biochem. Sci. 32 2007 217 224 (Pubitemid 46694328)
25. R.V. Pappu, and X. Wang S.L. Crick A polymer physics perspective on driving forces and mechanisms for protein aggregation Arch. Biochem. Biophys. 469 2008 132 141 (Pubitemid 350212851)
26. S.L. Crick, and M. Jayaraman R.V. Pappu Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions Proc. Natl. Acad. Sci. USA 103 2006 16764 16769 (Pubitemid 44737327)
27. A.H. Mao, and S.L. Crick R.V. Pappu Net charge per residue modulates conformational ensembles of intrinsically disordered proteins Proc. Natl. Acad. Sci. USA 107 2010 8183 8188
28. A. Möglich, K. Joder, and T. Kiefhaber End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation Proc. Natl. Acad. Sci. USA 103 2006 12394 12399 (Pubitemid 44267270)
29. S- and β-casein Biochemistry 44 2005 17027 17036 (Pubitemid 43007231)
30. H. Ecroyd, and T. Koudelka J.A. Carver Dissociation from the oligomeric state is the rate-limiting step in fibril formation by κ-casein J. Biol. Chem. 283 2008 9012 9022
31. J. Leonil, and G. Henry J.L. Putaux Kinetics of fibril formation of bovine κ-casein indicate a conformational rearrangement as a critical step in the process J. Mol. Biol. 381 2008 1267 1280
32. C. Atanasiu, and T.-J. Su D.T. Dryden Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme Nucleic Acids Res. 30 2002 3936 3944
33. E.N. Hudson, and G. Weber Synthesis and characterization of two fluorescent sulfhydryl reagents Biochemistry 12 1973 4154 4161
34. S. Campioni, and B. Mannini F. Chiti A causative link between the structure of aberrant protein oligomers and their toxicity Nat. Chem. Biol. 6 2010 140 147
35. M.K. Han, and J.R. Knutson L. Brand Sugar transport by the bacterial phosphotransferase system. Fluorescence studies of subunit interactions of enzyme I J. Biol. Chem. 265 1990 1996 2003
36. D.H.A. Corrêa, and C.H.I. Ramos The use of circular dichroism spectroscopy to study protein folding, form and function J. Biochem. 3 2009 164 173
37. K. Kawahara, and C. Tanford Viscosity and density of aqueous solutions of urea and guanidine hydrochloride J. Biol. Chem. 241 1966 3228 3232
38. C. Holt Structure and stability of bovine casein micelles Adv. Protein Chem. 43 1992 63 151
39. I.M. Reid Corpora amylacea of the bovine mammary gland. Histochemical and electron microscopic evidence for their amyloid nature J. Comp. Pathol. 82 1972 409 413
40. J.R. Lakowicz Principles of Fluorescence Spectroscopy 3rd ed. 2006 Springer New York
41. A. Saxena, J.B. Udgaonkar, and G. Krishnamoorthy Protein dynamics and protein folding dynamics revealed by time-resolved fluorescence M. Hof, R. Hutterer, V. Fidler, Fluorescence Spectroscopy in Biology. Advanced Methods and their Applications to Membranes, Proteins, DNA, and Cells 2005 Springer-Verlag New York 163 179
42. D.K. Wilkins, and S.B. Grimshaw L.J. Smith Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques Biochemistry 38 1999 16424 16431
43. N.J. Turro Modern Molecular Photochemistry 1991 University Science Books Sausalito, CA
44. R. Krishnan, and S.L. Lindquist Structural insights into a yeast prion illuminate nucleation and strain diversity Nature 435 2005 765 772 (Pubitemid 40839721)
45. J.D. Drury, and V. Narayanaswami Examination of lipid-bound conformation of apolipoprotein E4 by pyrene excimer fluorescence J. Biol. Chem. 280 2005 14605 14610 (Pubitemid 40562805)
46. A.B. Patel, P. Khumsupan, and V. Narayanaswami Pyrene fluorescence analysis offers new insights into the conformation of the lipoprotein-binding domain of human apolipoprotein E Biochemistry 49 2010 1766 1775
47. S. Thirunavukkuarasu, E.A. Jares-Erijman, and T.M. Jovin Multiparametric fluorescence detection of early stages in the amyloid protein aggregation of pyrene-labeled α-synuclein J. Mol. Biol. 378 2008 1064 1073
48. S.J. Hagen, and W.A. Eaton Two-state expansion and collapse of a polypeptide J. Mol. Biol. 301 2000 1019 1027
49. H.T. Tran, A. Mao, and R.V. Pappu Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins J. Am. Chem. Soc. 130 2008 7380 7392 (Pubitemid 351813231)
50. D.P. Teufel, and C.M. Johnson H. Neuweiler Backbone-driven collapse in unfolded protein chains J. Mol. Biol. 409 2011 250 262
51. A.S. Morar, and A. Olteanu G.J. Pielak Solvent-induced collapse of α-synuclein and acid-denatured cytochrome c Protein Sci. 10 2001 2195 2199 (Pubitemid 32988636)
52. J.C. Lee, and R. Langen J.R. Winkler α-Synuclein structures from fluorescence energy-transfer kinetics: implications for the role of the protein in Parkinsons disease Proc. Natl. Acad. Sci. USA 101 2004 16466 16471 (Pubitemid 39557736)