Diffusion on fractal lattices - A statistical model of chemical reactions involving proteins

Acta Physica Polonica B

Volumn 28, Issue 8, 1997, Pages 1853-1889

  Kurzynski M ^a  

^a ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0010467416     PISSN: 05874254     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Article

References (105)

1. W.P. Jencks, Catalysis in Chemistry and Enzymology, McGraw-Hill, New York 1969.
2. A. Fersht, Enzyme Structure and Mechanism, 2nd edn., Freeman, New York 1985.
3. J.A. McCammon, S.C. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University, Cambridge 1987.
4. C.L. Brooks III, M. Karplus, B.M. Pettitt, Proteins: a Theoretical Perspective of Dynamics, Structure and Thermodynamics, Advances in Chemical Physics vol. 71, Wiley, New York 1988.
5. H. Frauenfelder, F. Parak, R.D. Young, Annu. Rev. Biophys. Biophys. Chem. 17, 451 (1988).
6. H. Frauenfelder, P.J. Steinbach, R.D. Young, Chem. Scr. 29A, 145 (1989).
7. H. Frauenfelder, S.G. Sugar, P.G. Wolynes, Science 254, 1598 (1991).
8. M. Kurzyński, Prog. Biophys. Mol. Biol., review article submitted for publication.
9. M. Kurzyński, FEBS Lett. 328, 221 (1993).
10. M. Kurzyński, in: Diffusion processes - Experiment, Theory, Simulations, ed. A. Pȩkalski, p. 295, Lecture Notes in Physics, vol. 438, Springer, Berlin 1994.
11. M. Kurzyński, Biophys. Chem., in print.
12. T.E. Creighton, Proteins, Freeman, New York 1983.
13. M. Levitt, J. Mol. Biol. 168, 621 (1983).
14. B. Cartling, J. Chem. Phys. 91, 427 (1989).
15. J. Schlitter, Chem. Phys. 120, 187 (1988).
16. R.H. Austin, K.W. Beeson, L. Eisenstein, H. Frauenfelder, I.C. Gunsalus, Biochemistry 14, 5355 (1975).
17. L.S. Liebovitch, J. Fischbarg, J.P. Koniarek, I. Todorova, M. Wang, Biochim. Biophys. Acta 896, 173 (1987).
18. L.S. Liebovitch, J.M. Sullivan, Biophys. J. 52, 979 (1987).
19. R. McGee, M.S.P. Sansom, P.N.R. Usherwood, J. Membr. Biol. 102, 4 (1988).
20. M.S.P. Sansom, F.B. Ball, C.J. Kerry, R. McGee, R.L. Ramsey, P.N.R. Usherwood, Biophys. J. 56, 1229 (1989).
21. L.S. Liebovitch, J. Stat. Phys. 70, 329 (1993).
22. E.W. Montroll, B.J. West, in: Fluctuation phenomena, eds. E.W. Montroll and J. L. Lebowitz, updated edn., p. 61, North-Holland, Amsterdam 1987.
23. M.F. Schlesinger, Annu. Rev. Phys. Chem. 39, 269 (1988).
24. A. Blumen, H. Schnörer, Angew. Chem. Int. Ed. 29, 113 (1990).
25. A. Ansari, J. Berendzen, S.E. Bowne, H. Frauenfelder, I.E.T. Iben, T.B. Sauke, E. Shyamsunder, R.D. Young, Proc. Natl. Acad. Sci. USA 82, 5000 (1985).
26. P.J. Steinbach, A. Ansari, J. Berendzen, D. Braunstein, K. Chu, B.R. Cowen, D. Ehrenstein, H. Frauenfelder, J.B. Johnson, D.C. Lamb, S. Luck, J.R. Mourant, G.U. Nienhaus, P. Ormos, R. Philipp, A. Xie, R.D. Young, Biochemistry 30, 3988 (1991).
27. F. Post, W. Doster, G. Karvounis, M. Settles, Diophys. J. 64, 1833 (1993).
28. G.M. Mrevlishvili, Usp. Fiz. Nauk 128, 273 (1979)
29. [Sov. Phys. Usp. 22, 433 (1979)].
30. G.P. Singh, H.H. Schink, U.V. Löhneysen, F. Parak, S. Hunklinger, Z. Phys. B55, 23 (1989).
31. V.N. Morozov, S.G. Gevorkian, Biopolymers 24, 1785 (1985).
32. M. Settles, F. Post, D. Müller, A. Schulte, W. Doster, Biophys. Chem. 43, 107 (1992).
33. F. Parak, E.W. Knapp, D. Kucheida, J. Mol. Biol. 161, 177 (1982).
34. F. Parak, L. Reinisch, in: Methods in Enzymology, eds. C.H.W. Hirs, S.N. Timascheff, vol. 131, p. 568, Academic, London 1986.
35. W. Doster, S. Cusack, W. Petty, Nature 337, 754 (1989).
36. S. Cusack, Chem. Scr. 29A, 103 (1989).
37. W. Doster, S. Cusack, W. Petty, Phys. Rev. Lett. 65, 1080 (1990).
38. W. Doster, Mod. Phys. Lett. B5, 1407 (1991).
39. J.E. Straub, D. Thirmualai, Proc. Natl. Acad. Sci. USA 90, 809 (1993);
40. Proteins 15, 360 (1993).
41. N. Gö, T. Noguti, Chem. Scr. 29A, 151 (1989);
42. Proteins 5, 97 (1989).
43. A.E. Garcia, Proceedings of the Conference held at Centre de Physique des Houches, France, submitted (1995).
44. R. Elber, M. Karplus, Science 235, 318 (1987).
45. R. Rammal, G. Toulouse, M.A. Virasoro, Rev. Mod. Phys. 58, 765 (1986).
46. D.L. Stein, Phys. Scr. 34, 92 (1986).
47. D.L. Stein, Spin Glasses in Biology, World Scientific, Singapore 1992.
48. J.D. Bryngelson, P.G. Wolynes, J. Phys. Chem. 93, 6902 (1989).
49. J.J. Hopfield, Proc. Natl. Acad. Sci. USA 79, 2554 (1982).
50. M.S. Friedrichs, P.G. Wolynes, Science 246, 371 (1989).
51. M.S. Friedrichs, R.A. Goldstein, P.G. Wolynes, J. Mol. Biol. 222, 1013 (1991).
52. R. Lumry, R.B. Gregory, in: The Fluctuating Enzyme, ed. G.R. Welch, p. 1, Wiley, New York 1986.
53. P. Läuger, Biophys. J. 53, 877 (1988).
54. R. Elber, in: The Fractal Approach to Heterogeneous Chemistry, ed. D. Avnir, p. 407, Wiley, Chichester 1989.
55. J.T. Colvin, H.J. Stapleton, J. Chem. Phys. 82, 4699 (1985).
56. G. Careri, A. Giansanti, J.A. Rupley, Proc. Natl. Acad. Sci. USA 83, 6810 (1986);
57. Phys. Rev. A37, 2703 (1988).
58. M. Settles, W. Doster, F. Kremer, F. Post, W. Schirmacher, Philos. Mag. B65, 861 (1992).
59. R. Rammal, G. Toulouse, J. Phys. (Paris) Lett. 44, L13 (1983).
60. R. Rammal, J. Stat. Phys. 36, 547 (1984).
61. S. Alexander, R. Orbach, J. Phys. (Paris) Lett. 43, L625 (1982).
62. T. Nakayama, K. Yakubo, R.L. Orbach, Rev. Mod. Phys. 53, 175 (1991).
63. G.L. Millhauser, E.E. Salpeter, R.E. Oswald, Proc. Natl. Acad. Sci. USA 85, 1503 (1988).
64. C.A. Condat, J. Jäckle, Biophys. J. 55, 915 (1989).
65. D.G. Levitt, Biophys. J. 55, 489 (1989).
66. G.L. Millhauser, Biophys. J. 57, 857 (1990).
67. W. Doster, Ch. Holzhey, H. Miesmer, F. Post, J. Biol. Phys. 17, 281 (1990).
68. W. Doster, W. Schirmacher, M. Settles, Biophys. J. 57, 681 (1990).
69. W. Doster, W. Schirmacher, Comments Theor. Biol. 2, 261 (1991).
70. N.G. van Kampen, Stochastic Processes in Physics and Chemistry, North-Holland, Amsterdam 1981.
71. C.W. Gardiner, Handbook of Stochastic Methods, Springer Series in Synergetics vol. 13, Berlin 1983.
72. M. Smoluchowski, Z. Phys. Chem. 92, 129 (1917).
73. H.A. Kramers, Physica 7, 284 (1940).
74. E.W. Montroll, K.E. Shuler, Adv. Chem. Phys. 1, 361 (1958).
75. B. Widom, Science 148, 1555 (1965);
76. J. Chem. Phys. 55, 44 (1971).
77. S.H. Northrup, J.T. Hynes, J. Chem. Phys. 73, 2700 (1980).
78. M. Kurzyński, J. Chem. Phys. 93, 6793 (1990).
79. T. Yamamoto, J. Chem. Phys. 33, 281 (1960).
80. D. Chandler, J. Chem. Phys. 68, 2959 (1978).
81. S. Glasstone, K.J. Laidler, H. Eyring, The Theory of Rate Processes, McGraw-Hill, New York 1941.
82. P. Hänggi, P. Talkner, M. Borkovec, Rev. Mod. Phys. 62, 251 (1990).
83. D.N. Zubarev, Nonequilibrium Statistical Thermodynamics, Consultants Bureau, New York 1974.
84. A.A. Zharikov, S.I. Temkin, A.I. Burshtein, Chem. Phys. 103, 1 (1986).
85. R. Zwanzig, Acc. Chem. Res. 23, 148 (1990).
86. T.G. Dewey, Chem. Phys. 161, 339 (1992).
87. N. Agmon, J.J. Hopfield, J. Chem. Phys. 78, 6947 (1983).
88. R. Zwanzig, J. Chem. Phys. 97, 3587 (1992).
89. A. Fuliński, Phys. Lett. A180, 94 (1993).
90. A.A. Zharikov, S.F. Fischer, Chem. Phys. Lett. 249, 459 (1996).
91. A. Plonka, Time-Dependent Reactivity of Species in Condensed Media, Lecture Notes in Chemistry vol. 40, Springer, Berlin 1986.
92. D. Beece, L. Eisenstein, H. Frauenfelder, D. Good, M.C. Marden, L. Reinisch, A.H. Reynolds, L.B. Sorensen, K.T. Yue, Biochemistry 19, 5147 (1980).
93. B.B. Mandelbrot, The Fractal Geometry of Nature, Freeman, San Francisco 1982.
94. C. Kittel, Introduction to Solid State Physics, Wiley, New York 1966.
95. J. Klafter, A. Blumen, G. Zumofen, J. Stat. Phys. 36, 561 (1984).
96. G. Zumofen, A. Blumen, J. Klafter, J. Chem. Phys. 82, 3198 (1985).
97. R. Kopelman, J. Stat. Phys., 42, 185 (1986);
98. Science 241, 1620 (1988).
99. W. Nadler, D.L. Stein, Proc. Natl. Acad. Sci. USA 88, 6750 (1991).
100. M. Kurzyński, K. Palacz, P. Chelminiak, FEBS Lett., sub. for publication.
101. K. Palacz, M. Kurzyński, P. Chelminiak, M. Górny, Acta Phys. Pol. B28, (1997), this issue.
102. M. Abramowitz, I.A. Stegun, eds., Handbook of Mathematical Functions, Appl. Math. Series vol. 55, Natl. Bur. Stand., Dover 1964.
103. W. Schirmacher, Ber. Bunsenges. Phys. Chem. 95, 368 (1991).
104. J. Ninio, Proc. Natl. Acad. Sci. USA 84, 663 (1987).
105. F.W. Byron, R.W. Fuller, Mathematics of Classical and Quantum Physics, vol.2, Addison-Wesley, Reading 1968.