RNA topology remolds electrostatic stabilization of viruses

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

Volumn 89, Issue 3, 2014, Pages

  Erdemci Tandogan, Gonca ^a   Wagner, Jef ^a   Van Der Schoot, Paul ^b,c   Podgornik, Rudolf ^d,e   Zandi, Roya ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b EINDHOVEN UNIVERSITY OF TECHNOLOGY   (Netherlands)

^c UTRECHT UNIVERSITY   (Netherlands)

^d JO EF STEFAN INSTITUTE   (Slovenia)

^e UNIVERSITY OF LJUBLJANA   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROSTATICS; GENES; PROTEINS; VIRUSES;

BRANCHED RNA; CAPSID PROTEINS; CELLULAR RNA; ELECTROSTATIC STABILIZATION; HOST CELLS; NEGATIVELY CHARGED; POSITIVELY CHARGED; PROTEIN SHELLS;

RNA;

CAPSID PROTEIN; VIRUS RNA;

BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; GENETICS; RNA STABILITY; STATIC ELECTRICITY; VIRUS REPLICATION;

CAPSID PROTEINS; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, GENETIC; RNA STABILITY; RNA, VIRAL; STATIC ELECTRICITY; VIRUS REPLICATION;

EID: 84898961689     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.89.032707     Document Type: Article

References (42)

1. J. B. Bancroft, Adv. Virus Res. 16, 99 (1970). 9780-1203 10.1016/S0065-3527(08)60022-6
2. R. F. Bruinsma, Euro. Phys. J. E 19, 303 (2006). EPJSFH 1292-8941 10.1140/epje/i2005-10071-1
3. F. D. Sikkema, M. Comellas-Aragones, R. G. Fokkink, B. J. M. Verduin, J. Cornelissen, and R. J. M. Nolte, Org. Biomol. Chem. 5, 54 (2007). 1477-0520 10.1039/b613890j (Pubitemid 44927099)
4. Y. P. Ren, S. M. Wong, and L. Y. Lim, J. Gen. Virol. 87, 2749 (2006). JGVIAY 0022-1317 10.1099/vir.0.81944-0
5. P. Ni, Z. Wang, X. Ma, N. C. Das, P. Sokol, W. Chiu, B. Dragnea, M. Hagan, and C. C. Kao, J. Mol. Biol. 419, 284 (2012). JMOBAK 0022-2836 10.1016/j.jmb.2012.03.023
6. P. van der Schoot and R. Zandi, Phys. Biol. 4, 296 (2007). 1478-3975 10.1088/1478-3975/4/4/006
7. A. Losdorfer Bozic, A. Siber, and R. Podgornik, J. Biol. Phys. 39, 215 (2013). JBPHBZ 0092-0606 10.1007/s10867-013-9302-3
8. M. C. Daniel, I. B. Tsvetkova, Z. T. Quinkert, A. Murali, M. De, V. M. Rotello, C. C. Kao, and B. Dragnea, ACS Nano 4, 3853 (2010). 1936-0851 10.1021/nn1005073
9. A. Zlotnick, R. Aldrich, J. M. Johnson, P. Ceres, and M. J. Young, Virology 277, 450 (2000). EMVRAE 0042-6822 10.1006/viro.2000.0619
10. H.-K. Lin, P. van der Schoot, and R. Zandi, Phys. Biol. 9, 066004 (2012). 1478-3967 10.1088/1478-3975/9/6/066004
11. M. Comas-Garcia, R. D. Cadena-Nava, A. L. N. Rao, C. M. Knobler, and W. M. Gelbart, J. Virol. 86, 12271 (2012). 0022-538X 10.1128/JVI.01695-12
12. A. M. Yoffe, P. Prinsen, A. Gopal, C. M. Knobler, W. M. Gelbart, and A. Ben-Shaul, Pub. Natl. Acad. Sci. USA 105, 16153 (2008). PNASA6 0027-8424 10.1073/pnas.0808089105
13. F. Li Tai, W. M. Gelbart, and A. Ben-Shaul, J. Chem. Phys. 135, 155105 (2011). JCPSA6 0021-9606 10.1063/1.3652763
14. T. Hu, R. Zhang, and B. I. Shklovskii, Physica A 387, 3059 (2008). PHYADX 0378-4371 10.1016/j.physa.2008.01.010
15. P. van der Schoot and R. Bruinsma, Phys. Rev. E 71, 061928 (2005). PLEEE8 1539-3755 10.1103/PhysRevE.71.061928 (Pubitemid 41663788)
16. V. A. Belyi and M. Muthukumar, Pub. Natl. Aacad. Sci. USA 103, 17174 (2006). PNASA6 0027-8424 10.1073/pnas.0608311103 (Pubitemid 44788942)
17. C. L. Ting, J. Z. Wu, and Z. G. Wang, Pub. Natl. Aacad. Sci. USA 108, 16986 (2011). PNASA6 0027-8424 10.1073/pnas.1109307108
18. Y. F. Hu, R. Zandi, A. Anavitarte, C. M. Knobler, and W. M. Gelbart, Biophys. J. 94, 1428 (2008). BIOJAU 0006-3495 10.1529/biophysj.107.117473
19. R. D. Cadena-Nava, Y. F. Hu, R. F. Garmann, B. Ng, A. N. Zelikin, C. M. Knobler, and W. M. Gelbart, J. Phys. Chem. B 115, 2386 (2011). JPCBFK 1520-6106 10.1021/jp1094118
20. R. Zandi and P. van der Schoot, Biophys. J. 96, 9 (2009). BIOJAU 0006-3495 10.1529/biophysj.108.137489
21. A. L. Bozic, A. Siber, and R. Podgornik, J. Biol. Phys. 38, 657 (2012). JBPHBZ 0092-0606 10.1007/s10867-012-9278-4
22. A. Siber and R. Podgornik, Phys. Rev. E 78, 051915 (2008). PLEEE8 1539-3755 10.1103/PhysRevE.78.051915
23. O. M. Elrad and M. F. Hagan, Phys. Biol. 7, 045003 (2010). 1478-3975 10.1088/1478-3975/7/4/045003
24. M. F. Hagan, Adv. Chem. Phys. 155, 1 (2014).
25. A. Borodavka, R. Tuma, and P. G. Stockley, Pub. Natl. Acad. Sci. USA 109, 15769 (2012). PNASA6 0027-8424 10.1073/pnas.1204357109
26. P. G. Stockley, R. Twarock, S. E. Bakker, A. M. Barker, A. Borodavka, E. Dykeman, R. J. Ford, A. R. Pearson, S. E. V. Phillips, N. A. Ranson, J. Biol. Phys. 39, 277 (2013). JBPHBZ 0092-0606 10.1007/s10867-013-9313-0
27. A. McPherson, BioEssays 27, 447 (2005). BIOEEJ 0265-9247 10.1002/bies.20196 (Pubitemid 40592601)
28. I. Borukhov, D. Andelman, and H. Orland, Euro. Phys. J. B 5, 869 (1998). EPJBFY 1434-6028 10.1007/s100510050513
29. I. Borukhov, D. Andelman, and H. Orland, Europhys. Lett. 32, 499 (1995). EULEEJ 0295-5075 10.1209/0295-5075/32/6/007
30. I. Borukhov and D. Andelman, Macromolecules 31, 1665 (1998). MAMOBX 0024-9297 10.1021/ma9707300
31. I. Borukhov, D. Andelman, and H. Orland, J. Phys. Chem. B 103, 5042 (1999). JPCBFK 1520-6106 10.1021/jp990055r
32. A. Shafir, D. Andelman, and R. R. Netz, J. Chem. Phys. 119, 2355 (2003). JCPSA6 0021-9606 10.1063/1.1580798
33. T. C. Lubensky and J. Isaacson, Phys. Rev. A 20, 2130 (1979). 0556-2791 10.1103/PhysRevA.20.2130
34. T. T. Nguyen and R. F. Bruinsma, Phys. Rev. Lett. 97, 108102 (2006). PRLTAO 0031-9007 10.1103/PhysRevLett.97.108102 (Pubitemid 44373668)
35. S. I. Lee and T. T. Nguyen, Phys. Rev. Lett. 100, 198102 (2008). PRLTAO 0031-9007 10.1103/PhysRevLett.100.198102 (Pubitemid 351697484)
36. K. Elleuch, F. Lequeux, and P. Pfeuty, J. Phys. I France 5, 465 (1995). JPGCE8 1155-4304 10.1051/jp1:1995140
37. P.-G. de Gennes, Macromolecules 15, 492 (1982). MAMOBX 0024-9297 10.1021/ma00230a055
38. H. Ji and D. Hone, Macromolecules 21, 2600 (1988). MAMOBX 0024-9297 10.1021/ma00186a049
39. A. Siber, R. Zandi, and R. Podgornik, Phys. Rev. E 81, 051919 (2010). PLEEE8 1539-3755 10.1103/PhysRevE.81.051919
40. J. D. Perlmutter, C. Qiao, and M. F. Hagan, eLife 2, e00632 (2013). 2050-084X 10.7554/eLife.00632
41. I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P. Schuster, Monatsh. Chem. 125, 167 (1994). 0026-9247 10.1007/BF00818163
42. The standard deviation for the number of branch points in the ensemble of RNA secondary structures is around 2.5 for the RNA1 sequence of both BMV and CCMV.