The crowd you're in with: Effects of different types of crowding agents on protein aggregation

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1844, Issue 2, 2014, Pages 346-357

  Breydo, Leonid ^a   Reddy, Krishna D ^a   Piai, Alessandro ^b   Felli, Isabella C ^b   Pierattelli, Roberta ^b   Uversky, Vladimir N ^a,c  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b UNIVERSITY OF FLORENCE   (Italy)

^c INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

Author keywords

Amyloid; Crowding; Flexibility; Intrinsic disorder; Protein aggregation

Indexed keywords

CARBOHYDRATE; NUCLEIC ACID; POLYMER; POLYSACCHARIDE;

ARTICLE; ELECTRON MICROSCOPY; MACROMOLECULAR CROWDING; MACROMOLECULE; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE;

AMYLOID; CROWDING; FLEXIBILITY; INTRINSIC DISORDER; PROTEIN AGGREGATION;

ALPHA-SYNUCLEIN; AMYLOID; CELLULOSE; CHEMICAL PRECIPITATION; DEXTRANS; HISTONES; HUMANS; INSULIN; MURAMIDASE; POLYSACCHARIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION;

EID: 84890287425     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.11.004     Document Type: Article

References (64)

1. V.N. Uversky, and A.L. Fink Conformational constraints for amyloid fibrillation: the importance of being unfolded Biochim. Biophys. Acta 1698 2004 131 153
2. C. Liu, M. Zhao, L. Jiang, P.N. Cheng, J. Park, M.R. Sawaya, A. Pensalfini, D. Gou, A.J. Berk, C.G. Glabe, J. Nowick, and D. Eisenberg Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates Proc. Natl. Acad. Sci. U. S. A. 109 2012 20913 20918
3. A. Laganowsky, C. Liu, M.R. Sawaya, J.P. Whitelegge, J. Park, M. Zhao, A. Pensalfini, A.B. Soriaga, M. Landau, P.K. Teng, D. Cascio, C. Glabe, and D. Eisenberg Atomic view of a toxic amyloid small oligomer Science 335 2012 1228 1231
4. C.G. Glabe Structural classification of toxic amyloid oligomers J. Biol. Chem. 283 2008 29639 29643
5. R. Tycko Molecular structure of amyloid fibrils: insights from solid-state NMR Q. Rev. Biophys. 39 2006 1 55
6. H.X. Zhou, G. Rivas, and A.P. Minton Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences Annu. Rev. Biophys. 37 2008 375 397
7. R.J. Ellis, and A.P. Minton Protein aggregation in crowded environments Biol. Chem. 387 2006 485 497
8. L.A. Munishkina, A. Ahmad, A.L. Fink, and V.N. Uversky Guiding protein aggregation with macromolecular crowding Biochemistry 47 2008 8993 9006
9. L.A. Munishkina, E.M. Cooper, V.N. Uversky, and A.L. Fink The effect of macromolecular crowding on protein aggregation and amyloid fibril formation J. Mol. Recognit. 17 2004 456 464
10. C.F. Lee, S. Bird, M. Shaw, L. Jean, and D.J. Vaux Combined effects of agitation, macromolecular crowding, and interfaces on amyloidogenesis J. Biol. Chem. 287 2012 38006 38019
11. Q. Ma, J.B. Fan, Z. Zhou, B.R. Zhou, S.R. Meng, J.Y. Hu, J. Chen, and Y. Liang The contrasting effect of macromolecular crowding on amyloid fibril formation PLOS One 7 2012 e36288
12. P.S. Yeung, and P.H. Axelsen The crowded environment of a reverse micelle induces the formation of beta-strand seed structures for nucleating amyloid fibril formation J. Am. Chem. Soc. 134 2012 6061 6063
13. P.J. Flory Principles of Polymer Chemistry 1953 Cornell University Press Ithaca
14. C. Huang, G. Ren, H. Zhou, and C.C. Wang A new method for purification of recombinant human alpha-synuclein in Escherichia coli Protein Expr. Purif. 42 2005 173 177
15. S.E. Hill, T. Miti, T. Richmond, and M. Muschol Spatial extent of charge repulsion regulates assembly pathways for lysozyme amyloid fibrils PLoS One 6 2011 e18171
16. J.A. Cohlberg, J. Li, V.N. Uversky, and A.L. Fink Heparin and other glycosaminoglycans stimulate the formation of amyloid fibrils from alpha-synuclein in vitro Biochemistry 41 2002 1502 1511
17. L. Breydo, O.V. Bocharova, and I.V. Baskakov Semiautomated cell-free conversion of prion protein: applications for high-throughput screening of potential antiprion drugs Anal. Biochem. 339 2005 165 173
18. R.L.J. Keller The Computer Aided Resonance Assignment Tutorial, Cantina Verag 2004
19. J. Seeliger, A. Werkmuller, and R. Winter Macromolecular crowding as a suppressor of human IAPP fibril formation and cytotoxicity PLOS One 8 2013 e69652
20. Y. Hirata, Y. Sano, M. Aoki, H. Shohji, S. Katoh, J. Abe, S. Hitsukuri, and H. Yamamoto Small-angle X-ray scattering studies of moderately concentrated dextran solution Carbohydr. Polym. 53 2003 331 335
21. D. Venturoli, and B. Rippe Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability Am. J. Physiol. Renal Physiol. 288 2005 F605 F613
22. S. Mukherjee, M.M. Waegele, P. Chowdhury, L. Guo, and F. Gai Effect of macromolecular crowding on protein folding dynamics at the secondary structure level J. Mol. Biol. 393 2009 227 236
23. J.K. Armstrong, R.B. Wenby, H.J. Meiselman, and T.C. Fisher The hydrodynamic radii of macromolecules and their effect on red blood cell aggregation Biophys. J. 87 2004 4259 4270
24. M. James Physical Properties of Polymers Handbook 1996 American Institute of Physics Press Woodbury, NY
25. J.L. Whittingham, D.J. Scott, K. Chance, A. Wilson, J. Finch, J. Brange, and G.G. Dodson Insulin at pH 2: structural analysis of the conditions promoting insulin fibre formation J. Mol. Biol. 318 2002 479 490
26. B. Fauvet, M.K. Mbefo, M.B. Fares, C. Desobry, S. Michael, M.T. Ardah, E. Tsika, P. Coune, M. Prudent, N. Lion, D. Eliezer, D.J. Moore, B. Schneider, P. Aebischer, O.M. El-Agnaf, E. Masliah, and H.A. Lashuel Alpha-synuclein in central nervous system and from erythrocytes, mammalian cells, and Escherichia coli exists predominantly as disordered monomer J. Biol. Chem. 287 2012 15345 15364
27. T. Bartels, J.G. Choi, and D.J. Selkoe Alpha-synuclein occurs physiologically as a helically folded tetramer that resists aggregation Nature 477 2011 107 110
28. L. Breydo, J.W. Wu, and V.N. Uversky α-Synuclein misfolding and Parkinson's disease Biochim. Biophys. Acta 1822 2012 261 285
29. V.N. Uversky, J. Li, and A.L. Fink Evidence for a partially folded intermediate in alpha-synuclein fibril formation J. Biol. Chem. 276 2001 10737 10744
30. K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, and T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389 1997 251 260
31. L.A. Munishkina, A.L. Fink, and V.N. Uversky Conformational prerequisites for formation of amyloid fibrils from histones J. Mol. Biol. 342 2004 1305 1324
32. A.P. Butler, R.E. Harrington, and D.E. Olins Salt-dependent interconversion of inner histone oligomers Nucleic Acids Res. 6 1979 1509 1520
33. S. Kawashima, and K. Imahori Studies on histone oligomers. II. Reconstitution of heterotype histone oligomers and pH dependency of oligomer formation J. Biochem. (Tokyo) 88 1980 783 788
34. T.B. Topping, and L.M. Gloss The impact of solubility and electrostatics on fibril formation by the H3 and H4 histones Protein Sci. 20 2011 2060 2073
35. M. Malisauskas, V. Zamotin, J. Jass, W. Noppe, C.M. Dobson, and L.A. Morozova-Roche Amyloid protofilaments from the calcium-binding protein equine lysozyme: formation of ring and linear structures depends on pH and metal ion concentration J. Mol. Biol. 330 2003 879 890
36. E.A. Permyakov, and L.J. Berliner Alpha-lactalbumin: structure and function FEBS Lett. 473 2000 269 274
37. J. Li, S. Zhang, and C. Wang Only the reduced conformer of alpha-lactalbumin is inducible to aggregation by protein aggregates J. Biochem. (Tokyo) 129 2001 821 826
38. Y. Wang, M. Sarkar, A.E. Smith, A.S. Krois, and G.J. Pielak Macromolecular crowding and protein stability J. Am. Chem. Soc. 134 2012 16614 16618
39. L.A. Benton, A.E. Smith, G.B. Young, and G.J. Pielak Unexpected effects of macromolecular crowding on protein stability Biochemistry 51 2012 9773 9775
40. W. Bermel, M. Bruix, I.C. Felli, M.V.V. Kumar, R. Pierattelli, and S. Serrano Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins J. Biomol. NMR 55 2013 231 237
41. S. Sukenik, R. Politi, L. Ziserman, D. Danino, A. Friedler, and D. Harries Crowding alone cannot account for cosolute effect on amyloid aggregation PLOS One 6 2011 e15608
42. D.L. Zhang, L.J. Wu, J. Chen, and Y. Liang Effects of macromolecular crowding on the structural stability of human alpha-lactalbumin Acta Biochim. Biophys. Sin. (Shanghai) 44 2012 703 711
43. M. Jacob, and F.X. Schmid Protein folding as a diffusional process Biochemistry 38 1999 13773 13779
44. A. Ansari, C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton The role of solvent viscosity in the dynamics of protein conformational changes Science 256 1992 1796 1798
45. M. Sleutel, A.E.S. Van Driessche, W.C. Pan, E.K. Reichel, D. Maes, and P.G. Vekilov Does solution viscosity scale the rate of aggregation of folded proteins? J. Phys. Chem. Lett. 3 2012 1258 1263
46. H. Neuweiler, M. Lollmann, S. Doose, and M. Sauer Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy J. Mol. Biol. 365 2007 856 869
47. J.R. Wenner, and V.A. Bloomfield Crowding effects on EcoRV kinetics and binding Biophys. J. 77 1999 3234 3241
48. W. Dzwolak, S. Grudzielanek, V. Smirnovas, R. Ravindra, C. Nicolini, R. Jansen, A. Loksztejn, S. Porowski, and R. Winter Ethanol-perturbed amyloidogenic self-assembly of insulin: looking for origins of amyloid strains Biochemistry 44 2005 8948 8958
49. M. Bouchard, J. Zurdo, E.J. Nettleton, C.M. Dobson, and C.V. Robinson Formation of insulin amyloid fibrils followed by FTIR simultaneously with CD and electron microscopy Protein Sci. 9 2000 1960 1967
50. P. Neudecker, P. Robustelli, A. Cavalli, P. Walsh, P. Lundstrom, A. Zarrine-Afsar, S. Sharpe, M. Vendruscolo, and L.E. Kay Structure of an intermediate state in protein folding and aggregation Science 336 2012 362 366
51. 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
52. J.L. England, and G. Haran To fold or expand - a charged question Proc. Natl. Acad. Sci. U. S. A. 107 2010 14519 14520
53. K. Luger Structure and dynamic behavior of nucleosomes Curr. Opin. Genet. Dev. 13 2003 127 135
54. Z. Peng, M.J. Mizianty, B. Xue, L. Kurgan, and V.N. Uversky More than just tails: intrinsic disorder in histone proteins Mol. Biosyst. 8 2012 1886 1901
55. H.J. Li, R. Wickett, A.M. Craig, and I. Isenberg Conformational changes in histone IV Biopolymers 11 1972 375 397
56. A.C. Ferreon, and A.A. Deniz Alpha-synuclein multistate folding thermodynamics: implications for protein misfolding and aggregation Biochemistry 46 2007 4499 4509
57. A. Deleersnijder, M. Gerard, Z. Debyser, and V. Baekelandt The remarkable conformational plasticity of alpha-synuclein: blessing or curse? Trends Mol. Med. 19 2013 368 377
58. V.N. Uversky Under-folded proteins: conformational ensembles and their roles in protein folding, function, and pathogenesis Biopolymers 99 2013 870 887
59. M. Sarkar, C. Li, and G.J. Pielak Soft interactions and crowding Biophys. Rev. 5 2013 187 194
60. Y. Wang, L.A. Benton, V. Singh, and G.J. Pielak Disordered protein diffusion under crowded conditions J. Phys. Chem. Lett. 3 2012 2703 2706
61. K. Gekko, and T. Morikawa Preferential hydration of bovine serum albumin in polyhydric alcohol-water mixtures J. Biochem. (Tokyo) 90 1981 39 50
62. J. Chik, S. Mizrahi, S. Chi, V.A. Parsegian, and D.C. Rau Hydration forces underlie the exclusion of salts and of neutral polar solutes from hydroxypropylcellulose J. Phys. Chem. B 109 2005 9111 9118
63. K.D. Collins Sticky ions in biological systems Proc. Natl. Acad. Sci. U. S. A. 92 1995 5553 5557
64. D.W. Colby, K. Giles, G. Legname, H. Wille, I.V. Baskakov, S.J. DeArmond, and S.B. Prusiner Design and construction of diverse mammalian prion strains Proc. Natl. Acad. Sci. U. S. A. 106 2009 20417 20422