Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses

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

Volumn 78, Issue 5, 2008, Pages

  Šiber, Antonio ^a   Podgornik, Rudolf ^b,c  

^a INSTITUTE OF PHYSICS   (Croatia)

^b JO EF STEFAN INSTITUTE   (Slovenia)

^c UNIVERSITY OF LJUBLJANA   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROSTATICS; FLOW INTERACTIONS; MICROORGANISMS; NUCLEIC ACIDS; ORGANIC ACIDS; PROTEINS; RNA; SIZE DISTRIBUTION;

CHEMICAL SPECIFICITIES; DNA MOLECULES; ELECTROSTATIC INTERACTIONS; NONSPECIFIC INTERACTIONS; PROTEIN CHARGES; RNA VIRUSES; SALT CONCENTRATIONS; SPATIAL DISTRIBUTION OF; SPONTANEOUS ASSEMBLIES; VIRAL PROTEINS;

VIRUSES;

EID: 57049128122     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.78.051915     Document Type: Article

References (52)

1. D. L. D. Caspar and A. Klug, Cold Spring Harbor Symp. Quant. Biol. 27, 1 (1962).
2. A. Šiber, e-print arXiv:0711.3527.
3. G. J. Morgan, Trends Biochem. Sci. 28, 86 (2003). 10.1016/S0968-0004(02) 00007-5
4. A. Šiber, Nanotechnology 17, 3598 (2006). 10.1088/0957-4484/17/14/ 040
5. T. S. Baker, N. H. Olson, and S. D. Fuller, Microbiol. Mol. Biol. Rev. 63, 862 (1999).
6. E. Kellenberger, Eur. J. Biochem. 190, 233 (1990). 10.1111/j.1432-1033. 1990.tb15568.x
7. V. L. Lorman and S. B. Rochal, Phys. Rev. Lett. 98, 185502 (2007). 10.1103/PhysRevLett.98.185502
8. R. Twarock, J. Theor. Biol. 226, 477 (2004); 10.1016/j.jtbi.2003.10.006
9. R. Twarock, Philos. Trans. R. Soc. London, Ser. A 364, 3357 (2006). 10.1098/rsta.2006.1900
10. R. Zandi, P. van der Schoot, D. Reguera, W. Kegel, and H. Reiss, Biophys. J. 90, 1939 (2006). 10.1529/biophysj.105.072975
11. J. Groenewold and W. Kegel, J. Phys. Chem. B 105, 11702 (2001). 10.1021/jp011646w
12. J. Groenewold and W. Kegel, J. Phys.: Condens. Matter 16, S4877 (2004). 10.1088/0953-8984/16/42/006
13. H. Fraenkel-Conrat and R. C. Williams, Proc. Natl. Acad. Sci. U.S.A. 41, 690 (1955). 10.1073/pnas.41.10.690
14. R. F. Bruinsma, W. M. Gelbart, D. Reguera, J. Rudnick, and R. Zandi, Phys. Rev. Lett. 90, 248101 (2003). 10.1103/PhysRevLett.90.248101
15. W. K. Kegel and P. van der Schoot, Biophys. J. 86, 3905 (2004). 10.1529/biophysj.104.040055
16. A. Šiber and R. Podgornik, Phys. Rev. E 76, 061906 (2007). 10.1103/PhysRevE.76.061906
17. V. A. Belyi and M. Muthukumar, Proc. Natl. Acad. Sci. U.S.A. 103, 17174 (2006). 10.1073/pnas.0608311103
18. P. van der Schoot and R. Bruinsma, Phys. Rev. E 71, 061928 (2005). 10.1103/PhysRevE.71.061928
19. T. Hu, R. Zhang, and B. I. Shklovskii, Physica A 387, 3059 (2008). 10.1016/j.physa.2008.01.010
20. S. I. Lee and T. T. Nguyen, Phys. Rev. Lett. 100, 198102 (2008). 10.1103/PhysRevLett.100.198102
21. Y. Hu, R. Zandi, A. Anavitarte, C. M. Knobler, and W. Gelbart, Biophys. J. 94, 1428 (2008). 10.1529/biophysj.107.117473
22. I. Borukhov, D. Andelman, and H. Orland, J. Phys. Chem. B 103, 5042 (1999). 10.1021/jp990055r
23. A. Shafir, D. Andelman, and R. R. Netz, J. Chem. Phys. 119, 2355 (2003). 10.1063/1.1580798
24. P. G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University, Ithaca, 1979).
25. G. H. Fredrickson, The Equilibrium Theory of Inhomogeneous Polymers (Clarendon Press, Oxford, 2006).
26. R. Kumar and M. Muthukumar, J. Chem. Phys. 128, 184902 (2008). 10.1063/1.2917354
27. R. Podgornik, J. Polym. Sci., Part B: Polym. Phys. 42, 3539 (2004). 10.1002/polb.20205
28. S. F. Edwards, Proc. Phys. Soc. London 85, 613 (1965). 10.1088/0370-1328/85/4/301
29. A. V. Dobrynin and M. Rubinstein, Prog. Polym. Sci. 30, 1049 (2005). 10.1016/j.progpolymsci.2005.07.006
30. K. Iwasaki, B. L. Trus, P. T. Wingfield, N. Cheng, G. Campusano, V. B. Rao, and A. C. Steven, Virology 271, 321 (2000). 10.1006/viro.2000.0321
31. A. Zlotnick, N. Cheng, J. F. Conway, F. P. Booy, A. C. Steven, S. J. Stahl, and P. T. Wingfield, Biochemistry 35, 7412 (1996). 10.1021/bi9604800
32. B. S. Garbow, K. E. Hillstrom, and J. J. More, MINPACK library of FORTRAN routines, Argonne National Laboratory, MINPACK Project, 1996.
33. A. Zlotnik, N. Cheng, J. F. Conway, A. C. Steven, and P. T. Wingfield, Proc. Natl. Acad. Sci. U.S.A. 94, 9556 (1997). 10.1073/pnas.94.18.9556
34. M. Tihova, K. A. Dryden, T. L. Le, S. C. Harvey, J. E. Johnson, M. Yeager, and A. Schneeman, J. Virol. 78, 2897 (2004). 10.1128/JVI.78.6.2897-2905. 2004
35. N. Opalka, M. Tihova, C. Brugidou, A. Kumar, R. N. Beachy, C. M. Fauquet, and M. Yeager, J. Mol. Biol. 303, 197 (2000). 10.1006/jmbi.2000.4043
36. W. Zhang, S. Mukhopadhyay, S. V. Pletnev, T. S. Baker, R. J. Kuhn, and M. G. Rossmann, J. Virol. 76, 11645 (2002). 10.1128/JVI.76.22.11645-11658.2002
37. D. G. Angelescu, J. Stenhammar, and P. Linse, J. Phys. Chem. B 111, 8477 (2007). 10.1021/jp068384o
38. T. J. Smith, E. Chase, T. Schmidt, and K. L. Perry, J. Virol. 74, 7578 (2000). 10.1128/JVI.74.16.7578-7586.2000
39. http://www.rcsb.org
40. T. Hu and B. I. Shklovskii, Phys. Rev. E 75, 051901 (2007). 10.1103/PhysRevE.75.051901
41. R. F. Bruinsma, Eur. Phys. J. E 19, 303 (2006). 10.1140/epje/i2005-10071- 1
42. A. Evilevitch, M. Castelnovo, C. M. Knobler, and W. M. Gelbart, J. Phys. Chem. B 108, 6838 (2004). 10.1021/jp0376525
43. P. K. Purohit, M. M. Inamdar, P. D. Grayson, T. M. Squires, J. Kondev, and R. Phillips, Biophys. J. 88, 851 (2005). 10.1529/biophysj.104.047134
44. A. Šiber, M. Dragar, V. A. Parsegian, and R. Podgornik, Eur. Phys. J. E 26, 317 (2008). 10.1140/epje/i2008-10330-7
45. R. Podgornik and M. Ličer, Curr. Opin. Colloid Interface Sci. 11, 273 (2006). 10.1016/j.cocis.2006.08.001
46. W. K. Kegel and P. van der Schoot, Biophys. J. 91, 1501 (2006). 10.1529/biophysj.105.072603
47. J. Lidmar, L. Mirny, and D. R. Nelson, Phys. Rev. E 68, 051910 (2003). 10.1103/PhysRevE.68.051910
48. A. Šiber, Phys. Rev. E 73, 061915 (2006). 10.1103/PhysRevE.73. 061915
49. D. G. Angelescu and P. Linse, Phys. Rev. E 75, 051905 (2007). 10.1103/PhysRevE.75.051905
50. L. Tang, K. N. Johnson, L. A. Ball, T. Lin, M. Yeager, and J. E. Johnson, Nat. Struct. Biol. 8, 77 (2001). 10.1038/83089
51. G. J. Fleer, M. A. Cohen Stuart, J. M. H. M. Scheutjens, T. Cosgrove, and B. Vincent, Polymers at Interface (Chapman & Hall, London, 1993).
52. A. Zlotnick, R. Aldrich, J. M. Johnson, P. Ceres, and M. J. Young, Virology 277, 450 (2000). 10.1006/viro.2000.0619