Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments

Journal of Chemical Physics

Volumn 135, Issue 6, 2011, Pages

  Cohen, Samuel I A ^a   Vendruscolo, Michele ^a   Welland, Mark E ^a   Dobson, Christopher M ^a   Terentjev, Eugene M ^b   Knowles, Tuomas P J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID FIBRIL; ANALYTICAL APPROACH; ANALYTICAL EXPRESSIONS; CLOSED FORM; EXPERIMENTAL MEASUREMENTS; FIRST-PRINCIPLES; FITTING PROCEDURE; FIXED POINT ANALYSIS; FREE END; GENERAL ANALYTICAL SOLUTION; GROWTH LAWS; GROWTH SITES; KINETIC EQUATIONS; LAG TIME; LINEAR STRUCTURES; MOLECULAR LEVELS; NON-LINEAR; NUCLEATED POLYMERIZATION; SELF ASSEMBLY PROCESS; SELF-CONSISTENT SOLUTION; TIME EVOLUTIONS;

FUNCTIONAL POLYMERS; GLYCOPROTEINS; INTEGRAL EQUATIONS; KINETICS; MOLECULAR BIOLOGY; POLYMERIZATION; PROTEINS; SELF ASSEMBLY;

GROWTH KINETICS;

AMYLOID; BIOPOLYMER;

ARTICLE; CHEMISTRY; CRYSTALLIZATION; HUMAN; KINETICS; POLYMERIZATION; THEORETICAL MODEL;

AMYLOID; BIOPOLYMERS; CRYSTALLIZATION; HUMANS; KINETICS; MODELS, THEORETICAL; POLYMERIZATION;

EID: 80051866825     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3608916     Document Type: Article

References (109)

1. J. W. Gibbs, Trans. Conn. Acad. Arts Sci. 3, 108 (1876).
2. M. Volmer and A. Weber, Z. Phys. Chem. 119, 277 (1926). 10.1007/BF01379997
3. R. Kaischew and I. N. Stranski, Z. Phys. Chem., A 170, 295 (1934).
4. I. N. Stranski and R. Kaischew, Z. Phys. 36, 393 (1935). 10.1002/andp.19354150405
5. R. Becker and W. Dring, Ann. Phys. 26 (5), 719 (1935). 10.1002/andp.19354160806
6. M. Avrami, J. Chem. Phys. 7 (12), 1103 (1939). 10.1063/1.1750380
7. M. Avrami, J. Chem. Phys. 8 (2), 212 (1940). 10.1063/1.1750631
8. P. Flory, Principles of Polymer Chemistry (Cornell University Press, Ithaca, 1953).
9. P. Flory, Statistical Mechanics of Chain Molecules (Interscience, New York, 1969).
10. F. Oosawa and S. Asakura, Thermodynamics of the Polymerization of Protein (Academic Press, New York, 1975).
11. F. Oosawa and M. Kasai, J. Mol. Biol. 4, 10 (1962). 10.1016/S0022- 2836(62)80112-0
12. L. S. Tobacman and E. D. Korn, J. Biol. Chem. 258, 3207 (1983). 10.1097/00006254-198305000-00024
13. C. Frieden and D. W. Goddette, Biochemistry 22, 5836 (1983). 10.1021/bi00294a023
14. A. Wegner and J. Engel, Biophys. Chem. 3, 215 (1975). 10.1016/0301-4622(75)80013-5
15. J. Hofrichter, P. D. Ross, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. 71, 4864 (1974). 10.1073/pnas.71.12.4864
16. C. M. Dobson, Trends Biochem. Sci. 24, 329 (1999). 10.1016/S0968-0004(99) 01445-0 (Pubitemid 29421804)
17. F. Chiti and C. M. Dobson, Annu. Rev. Biochem. 75, 333 (2006). 10.1146/annurev.biochem.75.101304.123901 (Pubitemid 44118036)
18. C. M. Dobson, Nature (London) 426, 884 (2003). 10.1038/nature02261 (Pubitemid 38056880)
19. F. E. Cohen and J. W. Kelly, Nature (London) 426, 905 (2003). 10.1038/nature02265 (Pubitemid 38056884)
20. D. J. Selkoe, Nature (London) 426, 900 (2003). 10.1038/nature02264 (Pubitemid 38056883)
21. P. T. Lansbury and H. A. Lashuel, Nature (London) 443, 774 (2006). 10.1038/nature05290 (Pubitemid 44622681)
22. M. B. Pepys, Philos. Trans. R. Soc. London, Ser. B 356, 203 (2001). 10.1098/rstb.2000.0766 (Pubitemid 32241469)
23. J. Hardy and D. J. Selkoe, Science 297, 353 (2002). 10.1126/science. 1072994 (Pubitemid 34790756)
24. J. C. Sacchettini and J. W. Kelly, Nat. Rev. Drug Discovery 1, 267 (2002). 10.1038/nrd769
25. S. B. Prusiner, Science 252, 1515 (1991). 10.1126/science.1675487
26. J. H. Come, P. E. Fraser, and P. T. Lansbury, Proc. Natl. Acad. Sci. U.S.A. 90, 5959 (1993). 10.1073/pnas.90.13.5959
27. A. Aguzzi and C. Haass, Science 302, 814 (2003). 10.1126/science.1087348 (Pubitemid 37339613)
28. J. Falsig, K. P. Nilsson, T. P. J. Knowles, and A. Aguzzi, HFSP J. 2, 332 (2008). 10.2976/1.2990786
29. A. Aguzzi and T. O'Connor, Nat. Rev. Drug Discovery 9, 237 (2010). 10.1038/nrd3050
30. F. Oosawa, S. Asakura, K. Hotta, N. Imai, and T. Ooi, J. Poly. Sci. 37, 323 (1959). 10.1002/pol.1959.1203713202
31. M. Ataka, Prog. Cryst. Growth Charact. 30, 109 (1995). 10.1016/0960-8974(95)00013-W
32. H. Flyvbjerg, E. Jobs, and S. Leibler, Proc. Natl. Acad. Sci. U.S.A. 93, 5975 (1996). 10.1073/pnas.93.12.5975 (Pubitemid 26190787)
33. E. T. Powers and D. L. Powers, Biophys. J. 91, 122 (2006). 10.1529/biophysj.105.073767 (Pubitemid 44015313)
34. J. A. Cooper, E. L. Buhle, S. B. Walker, T. Y. Tsong, and T. D. Pollard, Biochemistry 22, 2193 (1983). 10.1021/bi00278a021
35. T. P. J. Knowles, T. W. Oppenheim, A. K. Buell, D. Y. Chirgadze, and M. E. Welland, Nat. Nanotechnol. 5, 204 (2010). 10.1038/nnano.2010.26
36. M. F. Bishop and F. A. Ferrone, Biophys. J. 46, 631 (1984). 10.1016/S0006-3495(84)84062-X
37. A. Wegner, J. Mol. Biol. 161, 217 (1982). 10.1016/0022-2836(82)90149-8 (Pubitemid 13253152)
38. A. Wegner, Nature (London) 296, 266 (1982). 10.1038/296266a0 (Pubitemid 12072147)
39. F. A. Ferrone, J. Hofrichter, and W. A. Eaton, J. Mol. Biol. 183, 611 (1985). 10.1016/0022-2836(85)90175-5 (Pubitemid 15036851)
40. F. A. Ferrone, J. Hofrichter, H. R. Sunshine, and W. A. Eaton, Biophys. J. 32, 361 (1980). 10.1016/S0006-3495(80)84962-9
41. F. A. Ferrone, J. Hofrichter, and W. A. Eaton, J. Mol. Biol. 183, 591 (1985). 10.1016/0022-2836(85)90174-3 (Pubitemid 15036850)
42. F. A. Ferrone, M. Ivanova, and R. Jasuja, Biophys. J. 82, 399 (2002). 10.1016/S0006-3495(02)75404-0
43. J. Hofrichter, J. Mol. Biol. 189, 553 (1986). 10.1016/0022-2836(86)90324- 4
44. T. Medkour, F. Ferrone, F. Galacttros, and P. Hannaert, Acta Biotheor. 56, 103 (2008). 10.1007/s10441-008-9032-2
45. S. R. Collins, A. Douglass, R. D. Vale, and J. S. Weissman, PLoS Biol. 2, e321 (2004). 10.1371/journal.pbio.0020321 (Pubitemid 39532919)
46. M. Tanaka, S. R. Collins, B. H. Toyama, and J. S. Weissman, Nature (London) 442, 585 (2006). 10.1038/nature04922 (Pubitemid 44167919)
47. S. Perrett and G. W. Jones, Curr. Opin. Struct. Biol. 18, 52 (2008). 10.1016/j.sbi.2007.12.005
48. Y. O. Chernoff, S. L. Lindquist, B. Ono, S. G. Inge-Vechtomov, and S. W. Liebman, Science 268, 880 (1995). 10.1126/science.7754373
49. J. T. Jarrett and P. T. Lansbury, Cell 73, 1055 (1993). 10.1016/0092-8674(93)90635-4 (Pubitemid 23180480)
50. J. D. Harper, C. M. Lieber, and P. T. Lansbury, Chem. Biol. 4, 951 (1997). 10.1016/S1074-5521(97)90303-3
51. M. A. Nowak, D. C. Krakauer, A. Klug, and R. M. May, Integr. Biol. 1, 3 (1998). 10.1002/(SICI)1520-6602(1998)1:13::AID-INBI23.0.CO;2-9
52. J. Collinge and A. R. Clarke, Science 318, 930 (2007). 10.1126/science.1138718 (Pubitemid 350098981)
53. I. V. Baskakov, FEBS J. 274, 3756 (2007). 10.1111/j.1742-4658.2007.05916. x (Pubitemid 47087672)
54. D. Hall and H. Edskes, J. Mol. Biol. 336, 775 (2004). 10.1016/j.jmb.2003.12.004 (Pubitemid 38183028)
55. W.-F. Xue, A. L. Hellewell, W. S. Gosal, S. W. Homans, E. W. Hewitt, and S. E. Radford, J. Biol. Chem. 284, 34272 (2009). 10.1074/jbc.M109.049809
56. W.-F. Xue, S. W. Homans, and S. E. Radford, Proc. Natl. Acad. Sci. U.S.A. 105, 8926 (2008). 10.1073/pnas.0711664105
57. C. F. Wright, S. A. Teichmann, J. Clarke, and C. M. Dobson, Nature (London) 438, 878 (2005). 10.1038/nature04195 (Pubitemid 41753072)
58. F. Ferrone, Methods Enzymol. 309, 256 (1999). 10.1016/S0076-6879(99) 09019-9 (Pubitemid 29446454)
59. T. P. J. Knowles, C. A. Waudby, G. L. Devlin, S. I. A. Cohen, A. Aguzzi, M. Vendruscolo, E. M. Terentjev, M. E. Welland, and C. M. Dobson, Science 326, 1533 (2009). 10.1126/science.1178250
60. N. Carulla, G. L. Caddy, D. R. Hall, J. Zurdo, M. Gair, M. Feliz, E. Giralt, C. V. Robinson, and C. M. Dobson, Nature (London) 436, 554 (2005). 10.1038/nature03986 (Pubitemid 41112928)
61. M. M. Pallitto and R. M. Murphy, Biophys. J. 81, 1805 (2001). 10.1016/S0006-3495(01)75831-6
62. T. Poeschel, N. V. Brilliantov, and C. Froemmel, Biophys. J. 85, 3460 (2003). 10.1016/S0006-3495(03)74767-5
63. K. C. Kunes, D. L. Cox, and R. R. P. Singh, Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 72, 051915 (2005). 10.1103/PhysRevE.72.051915 (Pubitemid 41777724)
64. M. E. Cates, J. Phys. Chem. 94, 371 (1990). 10.1021/j100364a063
65. R. Granek and M. E. Cates, J. Chem. Phys. 96, 4758 (1992). 10.1063/1.462787
66. A. Maestro, D. P. Acharya, H. Furukawa, J. M. Gutirrez, L.-Q. M. Arturo, M. Ishitobi, and H. Kunieda, J. Phys. Chem. B 108, 14009 (2004). 10.1021/jp048716u
67. D. Thusius, P. Dessen, and J. M. Jallon, J. Mol. Biol. 92, 413 (1975). 10.1016/0022-2836(75)90289-2
68. C. Ionescu-Zanetti, R. Khurana, J. R. Gillespie, J. S. Petrick, L. C. Trabachino, L. J. Minert, S. A. Carter, and A. L. Fink, Proc. Natl. Acad. Sci. U.S.A. 96, 13175 (1999). 10.1073/pnas.96.23.13175
69. R. Khurana, C. Ionescu-Zanetti, M. Pope, J. Li, L. Nielson, M. Ramrez-Alvarado, L. Regan, A. L. Fink, and S. A. Carter, Biophys. J. 85, 1135 (2003). 10.1016/S0006-3495(03)74550-0
70. S. I. A. Cohen, M. Vendruscolo, C. M. Dobson, and T. P. J. Knowles, J. Chem. Phys. 135, 065106 (2011). 10.1063/1.3608917
71. A. Lomakin, D. B. Teplow, D. A. Kirschner, and G. B. Benedek, Proc. Natl. Acad. Sci. U.S.A. 94, 7942 (1997). 10.1073/pnas.94.15.7942 (Pubitemid 27343754)
72. J. Masel, V. A. Jansen, and M. A. Nowak, Biophys. Chem. 77, 139 (1999). 10.1016/S0301-4622(99)00016-2 (Pubitemid 29206647)
73. J. F. Smith, T. P. J. Knowles, C. M. Dobson, C. E. Macphee, and M. E. Welland, Proc. Natl. Acad. Sci. U.S.A. 103, 15806 (2006). 10.1073/pnas. 0604035103 (Pubitemid 44657548)
74. E. Zeidler, Nonlinear Functional Analysis and its Applications: Part 1: Fixed-Point Theorems (Springer, New York, 1985).
75. A. Granas and J. Dugundji, Fixed Point Theory (Springer-Verlag, Berlin, 2003).
76. L. Nielsen, R. Khurana, A. Coats, S. Frokjaer, J. Brange, S. Vyas, V. N. Uversky, and A. L. Fink, Biochemistry 40, 6036 (2001). 10.1021/bi002555c (Pubitemid 32466306)
77. S. B. Padrick and A. D. Miranker, Biochemistry 41, 4694 (2002). 10.1021/bi0160462 (Pubitemid 34275671)
78. D. Hamada and C. M. Dobson, Protein Sci. 11, 2417 (2002). 10.1110/ps.0217702
79. R. Sabaté, M. Gallardo, and J. Estelrich, Biopolymers 71, 190 (2003). 10.1002/bip.10441
80. F. Librizzi and C. Rischel, Protein Sci. 14, 3129 (2005). 10.1110/ps.051692305 (Pubitemid 41770153)
81. C.-C. Lee, A. Nayak, A. Sethuraman, G. Belfort, and G. J. McRae, Biophys. J. 92, 3448 (2007). 10.1529/biophysj.106.098608 (Pubitemid 46698637)
82. M. A. Watzky, A. M. Morris, E. D. Ross, and R. G. Finke, Biochemistry 47, 10790 (2008). 10.1021/bi800726m
83. A. M. Morris, M. A. Watzky, and R. G. Finke, Biochim. Biophys. Acta 1794, 375 (2009). 10.1016/j.bbapap.2008.10.016
84. A. M. Morris, M. A. Watzky, J. N. Agar, and R. G. Finke, Biochemistry 47, 2413 (2008). 10.1021/bi701899y (Pubitemid 351304547)
85. A. M. Morris and R. G. Finke, Biophys. Chem. 140, 9 (2009). 10.1016/j.bpc.2008.11.003
86. S. I. A. Cohen, M. Vendruscolo, C. M. Dobson, and T. P. J. Knowles, arXiv:1107.1454 (2011).
87. E. H. C. Bromley, K. J. Channon, P. J. S. King, Z. N. Mahmoud, E. F. Banwell, M. F. Butler, M. P. Crump, T. R. Dafforn, M. R. Hicks, J. D. Hirst, A. Rodger, and D. N. Woolfson, Biophys. J. 98, 1668 (2010). 10.1016/j.bpj.2009.12. 4309
88. D. Kashchiev and S. Auer, J. Chem. Phys. 132, 215101 (2010). 10.1063/1.3447891
89. F. A. Ferrone, Methods Enzymol. 412, 285 (2006). 10.1016/S0076-6879(06) 12017-0 (Pubitemid 44548586)
90. S. K. R. M. P. Firestone and R. De Levie, J. Theor. Biol. 104, 553 (1983). 10.1016/0022-5193(83)90244-8
91. R. F. Goldstein and L. Stryer, Biophys. J. 50, 583 (1986). 10.1016/S0006-3495(86)83498-1
92. M. Ataka and T. Ogawa, J. Mater. Res. 11, 2889 (1993). 10.1557/JMR.1993.2889
93. Y. Bessho, M. Ataka, M. Asai, and T. Katsura, Biophys. J. 66, 310 (1994). 10.1016/S0006-3495(94)80779-9
94. R. M. Murphy and M. M. Pallitto, J. Struct. Biol. 130, 109 (2000). 10.1006/jsbi.2000.4253
95. S. Chen, F. A. Ferrone, and R. Wetzel, Proc. Natl. Acad. Sci. U.S.A. 99, 11884 (2002). 10.1073/pnas.182276099 (Pubitemid 34994493)
96. R. Wetzel, Acc. Chem. Res. 39, 671 (2006). 10.1021/ar050069h
97. J. M. Andrews and C. J. Roberts, J. Phys. Chem. B 111, 7897 (2007). 10.1021/jp070212j (Pubitemid 47169702)
98. T. R. Serio, A. G. Cashikar, A. S. Kowal, G. J. Sawicki, J. J. Moslehi, L. Serpell, M. F. Arnsdorf, and S. L. Lindquist, Science 289, 1317 (2000). 10.1126/science.289.5483.1317 (Pubitemid 30656041)
99. W. A. Eaton and J. Hofrichter, in Proceedings of the Symposium on Clinical and Biochemical Aspects of Hemoglobin Abnormalities (Academic Press, Inc., New York, 1978).
100. A. M. Ruschak and A. D. Miranker, Proc. Natl. Acad. Sci. U.S.A. 104, 12341 (2007). 10.1073/pnas.0703306104 (Pubitemid 47206139)
101. S. I. A. Cohen, M. Vendruscolo, C. M. Dobson, and T. P. J. Knowles, J. Chem. Phys. 135, 065107 (2011). 10.1063/1.3608918
102. K. Klement, K. Wieligmann, J. Meinhardt, P. Hortschansky, W. Richter, and M. Fndrich, J. Mol. Biol. 373, 1321 (2007). 10.1016/j.jmb.2007.08.068 (Pubitemid 47539491)
103. M. Fndrich, J. Mol. Biol. 365, 1266 (2007). 10.1016/j.jmb.2006.11.009 (Pubitemid 46048846)
104. J. Meinhardt, G. G. Tartaglia, A. Pawar, T. Christopeit, P. Hortschansky, V. Schroeckh, C. M. Dobson, M. Vendruscolo, and M. Fndrich, Protein Sci. 16, 1214 (2007). 10.1110/ps.062734207 (Pubitemid 46849229)
105. T. Ban, M. Hoshino, S. Takahashi, D. Hamada, K. Hasegawa, H. Naiki, and Y. Goto, J. Mol. Biol. 344, 757 (2004). 10.1016/j.jmb.2004.09.078 (Pubitemid 39469218)
106. T. Scheibel, A. S. Kowal, J. D. Bloom, and S. L. Lindquist, Curr. Biol. 11, 366 (2001). 10.1016/S0960-9822(01)00099-9 (Pubitemid 32200741)
107. A. H. DePace and J. S. Weissman, Nat. Struct. Biol. 9, 389 (2002). 10.1038/nsb786 (Pubitemid 34462559)
108. Y. Inoue, A. Kishimoto, J. Hirao, M. Yoshida, and H. Taguchi, J. Biol. Chem. 276, 35227 (2001). 10.1074/jbc.C100304200
109. A. Cacciuto, S. Auer, and D. Frenkel, Nature (London) 428, 404 (2004). 10.1038/nature02397 (Pubitemid 38419681)