Proteins as fractals: Role of the hydrodynamic interaction

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 83, Issue 2, 2011, Pages

  Granek, Rony ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOCORRELATION FUNCTIONS; FOLDED PROTEINS; HYDRODYNAMIC INTERACTION; MEAN SQUARE DISPLACEMENT; NEUTRON SPIN ECHO; TIME-DEPENDENT;

FLUID DYNAMICS; FRACTALS; HYDRODYNAMICS; REGRESSION ANALYSIS;

AMINO ACIDS;

EID: 79952511822     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.83.020902     Document Type: Article

References (37)

1. R. Elber and M. Karplus, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.56.394 56, 394 (1986).
2. M. B. Enright and D. M. Leitner, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.71.011912 71, 011912 (2005). (Pubitemid 40619971)
3. X. Yu and D. M. Leitner, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1626636 119, 12673 (2003);
4. D. M. Leitner, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.59.032607.093606 59, 233 (2008). (Pubitemid 351703386)
5. R. Burioni, D. Cassi, F. Cecconi, and A. Vulpiani, Proteins: Struct. Func. Bioinf. 18PLAF 0887-3585 10.1002/prot.20072 55, 529 (2004); (Pubitemid 38620078)
6. R. Burioni, D. Cassi, F. Cecconi, and A. Vulpiani, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2002-00445-5 58, 806 (2002).
7. R. Granek and J. Klafter, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.95.098106 95, 098106 (2005). (Pubitemid 41505889)
8. S. Reuveni, R. Granek, and J. Klafter, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.208101 100, 208101 (2008). (Pubitemid 351718017)
9. M. de Leeuw, S. Reuveni, J. Klafter, and R. Granek, PLoS ONE PRLTAO 1932-6203 10.1371/journal.pone.0007296 4, e7296 (2009).
10. S. Reuveni, R. Granek, and J. Klafter, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.1002018107 107, 13696 (2010).
11. A. Banerji and I. Ghosh, PLoS ONE PNASA6 1932-6203 10.1371/journal.pone. 0007361 4, e7361 (2009).
12. H. J. Stapleton, J. P. Allen, C. P. Flynn, D. G. Stinson, and S. R. Kurtz, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.45.1456 45, 1456 (1980).
13. S. G. Lushnikov, A. V. Svanidze, and I. L. Sashin, JETP Lett. JTPLA2 0021-3640 10.1134/1.2045334 82, 30 (2005). (Pubitemid 41337599)
14. S. C. Kou and X. S. Xie, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.180603 93, 180603 (2004);
15. W. Min, G. Luo, B. J. Cherayil, S. C. Kou, and X. S. Xie, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.198302 94, 198302 (2005). (Pubitemid 41493017)
16. J. Lal, P. Fouquet, M. Maccarini, and L. Makowski, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2010.01.029 397, 423 (2010).
17. P. Senet, G. G. Maisuradze, C. Foulie, P. Delarue, and H. A. Scheraga, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0810679105 105, 19708 (2008).
18. T. Neusius, I. Daidone, I. M. Sokolov, and J. C. Smith, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.188103 100, 188103 (2008). (Pubitemid 351656434)
19. D. Stauffer and A. Aharony, Introduction to Percolation Theory, 2nd ed. (Taylor & Francis, London, 1992).
20. S. Alexander and R. Orbach, J. Phys. Lett. JPSLBO 0302-072X 10.1051/jphyslet:019820043017062500 43, L625 (1982).
21. S. Alexander, Phys. Rev. B PLRBAQ 1098-0121 10.1103/PhysRevB.40.7953 40, 7953 (1989).
22. I. Bahar, A. R. Atilgan, and B. Erman, Folding Des. FODEFH 1359-0278 10.1016/S1359-0278(97)00024-2 2, 173 (1997);
23. I. Bahar, A. R. Atilgan, M. C. Demirel, and B. Erman, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.80.2733 80, 2733 (1998).
24. H. Morita and M. Takano, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.79.020901 79, 020901 (R) (2009).
25. M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (Clarendon, Oxford, 1986).
26. A. G. Zilman and R. Granek, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.58.R2725 58, R2725 (1998).
27. M. E. Cates, J. Phys. France JPRAAJ 0368-3842 10.1051/jphys: 019850046070105900 46, 1059 (1985).
28. A. Blumen, Ch. von Ferber, A. Jurjiu, and Th. Koslowski, Macromolecules MAMOBX 0024-9297 10.1021/ma034553g 37, 638 (2004);
29. A. Blumen, A. Jurjiu, Th. Koslowski, and Ch. von Ferber, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.67.061103 67, 061103 (2003).
30. A. Bunde, H. E. Roman, S. Russ, A. Aharony, and A. B. Harris, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.69.3189 69, 3189 (1992).
31. J. W. Kantelhardt and A. Bunde, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.56.6693 56, 6693 (1997).
32. f values containing about 5000 proteins see the supporting information in Ref. [7].
33. s [5].
34. c = 6 A, 1.2 (Mb) and 1.57 (Hb), give support to the Rouse exponent for Mb (0.40), while for Hb the Zimm exponent prevails (0.41).
35. A. H. Krall and D. A. Weitz, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.80.778 80, 778 (1998).
36. I. Webman and G. S. Grest, Phys. Rev. B PLRBAQ 1098-0121 10.1103/PhysRevB.31.1689 31, 1689 (1985).
37. P. Meakin, J. Phys. A JPHAC5 0305-4470 10.1088/0305-4470/17/18/008 17, L975 (1984).