Modeling capsid self-assembly: Design and analysis

Physical Biology

Volumn 7, Issue 4, 2010, Pages

  Rapaport, D C ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MIRIDAE;

ARTICLE; BIOLOGICAL MODEL; VIRUS ASSEMBLY; VIRUS CAPSID;

CAPSID; MODELS, BIOLOGICAL; VIRUS ASSEMBLY;

EID: 79551501748     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/7/4/045001     Document Type: Article

References (39)

1. Crick F H C and Watson J D 1956 The structure of small viruses Nature (Lond.) 177 473
2. Caspar D L D and Klug A 1962 Physical principles in the construction of regular viruses Cold Spring Harbor Symp. Quant. Biol. 27 1
3. Whitesides G M and Grzybowski B 2002 Self-assembly at all scales Science 295 2418
4. Caspar D L D 1980 Movement and self-control in protein assemblies: quasi-equivalence revisited Biophys. J. 32 103
5. Rapaport D C 2004 The Art of Molecular Dynamics Simulation 2nd edn (Cambridge: Cambridge University Press)
6. Endres D and Zlotnick A 2002 Model-based analysis of assembly kinetics for virus capsids and other spherical polymers Biophys. J. 83 1217
7. Baker T S, Olson N H and Fuller S D 1999 Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs Microbiol. Mol. Biol. Rev. 63 862
8. Fox J M, Johnson J E and Young M J 1994 RNA/protein interactions in icosahedral virus assembly Semin. Virol. 5 51
9. Prevelige P E, Thomas D and King J 1993 Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells Biophys. J. 64 824
10. Zlotnick A, Johnson J M, Wingfield P W, Stahl S J and Endres D 1999 A theoretical model successfully identifies features of hepatitis B virus capsid assembly Biochemistry 38 14644
11. Casini G L, Graham D, Heine D, Garcea R L and Wu D T 2004 In vitro papillomavirus capsid assembly analyzed by light scattering Virology 325 320
12. Speir J A, Munshi S, Wang G, Baker T S and Johnson J E 1995 Structure of the native and swollen forms of cowpea chlorotic mottle virus determined by x-ray crystallography and cryo-electron microscopy Structure 3 63
13. Johnson J E 1996 Functional implications of protein-protein interactions in icosahedral viruses Proc. Natl Acad. Sci. USA 93 27
14. Rapaport D C, Johnson J E and Skolnick J 1999 Supramolecular self-assembly: molecular dynamics modeling of polyhedral shell formation Comput. Phys. Commun. 121 231
15. Rapaport D C 2004 Self-assembly of polyhedral shells: a molecular dynamics study Phys. Rev. E 70 051905
16. Rapaport D C 2008 Role of reversibility in viral capsid growth: a paradigm for self-assembly Phys. Rev. Lett. 101 186101
17. Rapaport D C 2010 Studies of reversible capsid shell growth J. Phys.: Condens. Matter 22 104115
18. Nguyen H D, Reddy V S and Brooks C L III 2007 Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids Nano Lett. 7 338
19. Hagan M F and Chandler D 2006 Dynamic pathways for viral capsid assembly Biophys. J. 91 42
20. Schwartz R, Shor P W, Prevelige P E and Berger B 1998 Local rules simulation of the kinetics of virus capsid self-assembly Biophys. J. 75 2626
21. Wilber A W, Doye J P K, Louis A A, Noya E G, Miller M A and Wong P 2007 Reversible self-assembly of patchy particles into monodisperse icosahedral clusters J. Chem. Phys. 127 085106
22. Chen T, Zhang Z and Glotzer S C 2007 A precise packing sequence for self-assembled convex structures Proc. Natl Acad. Sci. USA 104 717
23. Johnston I G, Louis A A and Doye J P K 2010 Modelling the self-assembly of virus capsids J. Phys.: Condens. Matter 22 104101
24. Freddolino P L, Arkhipov A S, Larson S B, McPherson A and Schulten K 2006 Molecular dynamics simulations of the complete satellite tobacco mosaic virus Structure 14 437
25. Lidmar J, Mirny L and Nelson D R 2003 Virus shapes and buckling transitions in spherical shells Phys. Rev. E 68 051910
26. Twarock R 2004 A tiling approach to virus capsid assembly explaining a structural puzzle in virology J. Theor. Biol. 226 477
27. Zandi R, Reguera D, Bruinsma R F, Gelbart W M and Rudnick J 2004 Origin of icosahedral symmetry in viruses Proc. Natl Acad. Sci. USA 101 15556
28. Hicks S D and Henley C L 2006 Irreversible growth model for virus capsid assembly Phys. Rev. E 74 031912
29. Hemberg M, Yaliraki S N and Barahona M 2006 Stochastic kinetics of viral capsid assembly based on detailed protein structures Biophys. J. 90 3029
30. van der Schoot P and Zandi R 2007 Kinetic theory of virus capsid assembly Phys. Biol. 4 296
31. Williams R 1979 The Geometric Foundation of Natural Structure (New York: Dover)
32. Casjens S 1985 An introduction to virus structure and assembly Virus Structure and Assembly ed S Casjens (Boston: Jones and Bartlett) p 1
33. Rossmann M G and Erickson J W 1985 Structure and assembly of icosahedral shells Virus Structure and Assembly ed S Casjens (Boston: Jones and Bartlett) p 30
34. Reddy V S, Giesing H A, Morton R T, Kumar A, Post C B, Brooks III C L and Johnson J E 1998 Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses Biophys. J. 74 546
35. Zlotnick A, Aldrich R, Johnson J M, Ceres P and Young M J 2000 Mechanism of capsid assembly for an icosahedral plant virus Virology 277 450
36. Singh S and Zlotnick A 2003 Observed hysteresis of virus capsid disassembly is implicit in kinetic models of assembly J. Biol. Chem. 278 18249
37. Zlotnick A 1994 To build a virus capsid, an equilibrium model of the self assembly of polyhedral protein complexes J. Mol. Biol. 241 59
38. Rapaport D C 1987 Algorithms for lattice statistics Comput. Phys. Rep. 5 265
39. Endres D, Miyahara M, Moisant P and Zlotnick A 2005 A reaction landscape identifies the intermediates critical for self-assembly of virus capsids and other polyhedral structures Protein Sci. 14 1518