Electrostatics of capsid-induced viral RNA organization

Journal of Chemical Physics

Volumn 131, Issue 10, 2009, Pages

  Forrey, Christopher ^a   Muthukumar, M ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE-PAIRING; CAPSID PROTEINS; CHARGED POLYELECTROLYTES; CHARGED RESIDUES; COARSE GRAINED MODELS; ELECTROSTATIC INTERACTIONS; ELECTROSTATIC POTENTIALS; EXPERIMENTAL DATA; EXPERIMENTAL STUDIES; FLEXIBLE POLYELECTROLYTES; GENOME STRUCTURES; LANGEVIN DYNAMICS; N-TERMINALS; RNA SEQUENCES; RNA STRUCTURES; SECONDARY STRUCTURES; TOPOLOGICAL FEATURES; VIRAL GENOME; VIRAL RNA; WORK SUPPORT;

DISSOCIATION; ELECTROSTATICS; GENES; LOCATION; NUCLEIC ACIDS; POLYELECTROLYTES; RNA;

CRYSTAL STRUCTURE;

EID: 70349292371     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3216550     Document Type: Article

References (41)

1. A. Cann, Principles of Molecular Virology, 4th ed. (Academic, New York, 2005).
2. D. M. Knipe and P. M. Howley, Fundamental Virology, 4th ed. (Williams and Wilkins, Baltimore, 2001).
3. E. Hiebert and J. B. Bancroft, Virology 0042-6822 39, 296 (1969). 10.1016/0042-6822(69)90050-6
4. A. T. Da Poian, A. C. Oliveira, and J. L. Silva, Biochemistry 0006-2960 34, 2672 (1995). 10.1021/bi00008a034
5. A. Zlotnik and S. J. Stray, Trends Biotechnol. 0167-7799 21, 536 (2003). 10.1016/j.tibtech.2003.09.012 (Pubitemid 37415005)
6. D. E. Smith, S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, and C. Bustamante, Nature (London) 0028-0836 413, 748 (2001). 10.1038/35099581 (Pubitemid 33009954)
7. A. Evilevitch, M. Castelnovo, C. M. Knobler, and W. M. Gelbart, J. Phys. Chem. B 1089-5647 108, 6838 (2004). 10.1021/jp0376525
8. C. Forrey and M. Muthukumar, Biophys. J. 0006-3495 91, 25 (2006). 10.1529/biophysj.105.073429 (Pubitemid 44015306)
9. A. S. Petrov, K. Lin-Hing, and S. C. Harvey, Structure 15, 807 (2007). 10.1016/j.str.2007.05.005 0969-2126 (Pubitemid 47042427)
10. D. L. D. Casper and A. Klug, Cold Spring Harb. Symp. Quant. Biol. 27, 1 (1956). 0091-7451
11. V. Belyi and M. Muthukumar, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 17174 (2006). 10.1073/pnas.0608311103 (Pubitemid 44788942)
12. P. van der Schoot and R. Bruinsma, Phys. Rev. E 1063-651X 71, 061928 (2005). 10.1103/PhysRevE.71.061928
13. R. Bruinsma, Eur. Phys. J. E 1292-8941 19, 303 (2006). 10.1140/epje/i2005-10071-1
14. D. G. Angelescu and P. Linse, Soft Matter 1744-683X 4, 1981 (2008). 10.1039/b802597e
15. A. Siber and R. Podgornik, Phys. Rev. E 1063-651X 78, 051915 (2008). 10.1103/PhysRevE.78.051915
16. Z. D. Li, J. -Z. Wu, and Z. G. Wang, Biophys. J. 0006-3495 94, 737 (2008). 10.1529/biophysj.107.112508 (Pubitemid 351162444)
17. A. M. Yoffe, P. Prinsen, A. Gopla, C. M. Knobler, W. M. Gelbart, and A. Ben-Shaul, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 105, 16153 (2008). 10.1073/pnas.0808089105
18. Y. F. Hu, R. Zandi, A. Anavitarte, C. M. Knobler, and W. M. Gelbart, Biophys. J. 0006-3495 94, 1428 (2008). 10.1529/biophysj.107.117473
19. D. Störkle, S. Duschner, N. Heimann, M. Maskos, and M. Schmidt, Macromolecules 0024-9297 40, 7998 (2007). 10.1021/ma0711689 (Pubitemid 350099705)
20. R. B. Breitenkamp, Z. Ou, K. Breitenkamp, M. Muthukumar, and T. Emrick, Macromolecules 0024-9297 40, 7617 (2007). 10.1021/ma070714v (Pubitemid 350014289)
21. S. van den Worm, R. Koning, H. Warmenhoven, H. Koerten, and J. van Duin, J. Mol. Biol. 0022-2836 363, 858 (2006). 10.1016/j.jmb.2006.08.014 (Pubitemid 44436252)
22. N. Opalka, M. Tihova, C. Brugidou, A. Kumar, R. Beachy, C. Fauquet, and M. Yeager, J. Mol. Biol. 0022-2836 303, 197 (2000). 10.1006/jmbi.2000.4043 (Pubitemid 30809653)
23. R. Koning, S. van den Worm, J. Plaisier, J. van Duin, J. Abrahams, and H. Koerten, J. Mol. Biol. 0022-2836 332, 415 (2003). 10.1016/S0022-2836(03)00846-5 (Pubitemid 37013509)
24. Z. Chen, C. Stauffacher, Y. Li, T. Schmidt, B. Wu, G. Kamer, M. Shanks, G. Lomonossoff, and J. Johnson, Science 0036-8075 245, 154 (1989). 10.1126/science.2749253
25. A. Fisher and J. Johnson, Nature (London) 0028-0836 361, 176 (1993). 10.1038/361176a0 (Pubitemid 23031355)
26. S. Larson, R. Lucas, A. Greenwood, and A. McPherson, Virology 0042-6822 334, 245 (2005). 10.1016/j.virol.2005.01.036 (Pubitemid 40386958)
27. M. Rossman, F. Arisaka, A. Battisti, V. Bowman, and P. Chipman, Acta Crystallogr., Sect. D: Biol. Crystallogr. 0907-4449 D63, 9 (2007).
28. A. Schneemann, Annu. Rev. Microbiol. 0066-4227 60, 51 (2006). 10.1146/annurev.micro.60.080805.142304 (Pubitemid 44627940)
29. P. Freddolino, A. Arkhipov, S. Larson, A. McPherson, and K. Schulten, Structure (London) 0969-2126 14, 437 (2006). 10.1016/j.str.2005.11.014 (Pubitemid 43363477)
30. D. Zhang, R. Konecny, N. Baker, and J. McCammon, Biopolymers 0006-3525 75, 325 (2004). 10.1002/bip.20120
31. R. Konecny, J. Trylska, F. Tama, D. Zhang, N. Baker, C. Brooks, and J. McCammon, Biopolymers 0006-3525 82, 106 (2006). 10.1002/bip.20409
32. M. Tihova, K. Dryden, T. Le, S. Harvey, J. Johnson, M. Yeager, and A. Schneemann, J. Virol. 0022-538X 78, 2897 (2004). 10.1128/JVI.78.6.2897-2905.2004 (Pubitemid 38314347)
33. S. Larson, S. Koszelak, J. Day, A. Greenwood, J. Dodds, and A. Mcpherson, J. Mol. Biol. 0022-2836 231, 375 (1993). 10.1006/jmbi.1993.1289 (Pubitemid 23188260)
34. S. Larson, S. Koszelak, J. Day, A. Greenwood, J. Dodds, and A. Mcpherson, Nature (London) 0028-0836 361, 179 (1993). 10.1038/361179a0 (Pubitemid 23031356)
35. K. Johnson, L. Tang, J. Johnson, and L. Ball, J. Virol. 0022-538X 78, 11371 (2004). 10.1128/JVI.78.20.11371-11378.2004 (Pubitemid 39299678)
36. L. Tang, K. Johnson, L. Ball, T. Lin, M. Yeager, and J. Johnson, Nat. Struct. Biol. 8, 77 (2001). 10.1038/83089 (Pubitemid 32043033)
37. Q. Xia, J. Jakana, J. Zhang, and Z. Zhou, J. Biol. Chem. 0021-9258 278, 1094 (2003). 10.1074/jbc.M205964200 (Pubitemid 36790789)
38. B. Prasad, R. Rothnagel, C. Zeng, J. Jakana, J. Lawton, W. Chiu, and M. Estes, Nature (London) 0028-0836 382, 471 (1996). 10.1038/382471a0 (Pubitemid 26294969)
39. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, New York, 1996).
40. J. Rudnick and R. Bruinsma, Phys. Rev. Lett. 0031-9007 94, 038101 (2005). 10.1103/PhysRevLett.94.038101 (Pubitemid 40607333)
41. K. Toropora, G. Basnak, R. Twarock, P. G. Stockley, and N. A. Ranson, J. Mol. Biol. 0022-2836 375, 824 (2008). 10.1016/j.jmb.2007.08.067 (Pubitemid 350297278)