2007
DOI: 10.1021/nl062449h
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Deciphering the Kinetic Mechanism of Spontaneous Self-Assembly of Icosahedral Capsids

Abstract: Self-assembly of viral proteins into icosahedral capsids is an interesting yet poorly understood phenomenon of which elucidation may aid the exploration of beneficial applications of capsids in materials science and medicine. Using molecular dynamics simulations of coarse-grained models for capsid proteins, we show that the competition between the formation of full capsids and nonidealized structures is strongly dependent upon the protein concentration and temperature, occurring kinetically as a cascade of ele… Show more

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Cited by 191 publications
(317 citation statements)
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“…A variety of such misassembled structuressincluding dumbbellsshave also been observed in molecular dynamics simulations of coarse-grained models of capsid proteins. 9 These have been compared to socalled "monster" structures that were found in in vitro studies of the assembly of turnip crinkle virus and capsid protein around the viral RNA. 10 12 correspond to Caspar-Klug structures with T ) 1, 3, 4, and 7; a so-called pseudo-Caspar-Klug structure with T ) 2 is also known.…”
Section: Resultsmentioning
confidence: 99%
“…A variety of such misassembled structuressincluding dumbbellsshave also been observed in molecular dynamics simulations of coarse-grained models of capsid proteins. 9 These have been compared to socalled "monster" structures that were found in in vitro studies of the assembly of turnip crinkle virus and capsid protein around the viral RNA. 10 12 correspond to Caspar-Klug structures with T ) 1, 3, 4, and 7; a so-called pseudo-Caspar-Klug structure with T ) 2 is also known.…”
Section: Resultsmentioning
confidence: 99%
“…We show in appendix A that the average timescales of these phases for an individual capsid can be described by τ = τ nuc + τ elong , with and , where f is the subunit-subunit binding rate constant, C S is the concentration of free subunits, n nuc is the number of subunits in the nucleus. Because elongation requires N − n nuc assembly events, it introduces a minimum timescale for the overall assembly process, which is primarily responsible for the lag time in assembly kinetics reported in experiments [9,12,53], theory [21,48], and simulations [26,28,80], and results in a distribution of assembly times for an individual capsid that cannot be fit with a sum of pure exponential functions [81]. The observed assembly rate constant, f, can be considered an average quantity, since computational models [26,28] suggest that it varies for different intermediates and decreases due to excluded volume constraints as assembly nears completion.…”
Section: A the Kinetics Of Core-controlled Assemblymentioning
confidence: 99%
“…Thus, in addition to their biomedical and technological applications, studying viral capsids has revealed fundamental principles of assembly. Although specific assembly mechanisms are poorly understood for most viruses, a general mechanism has emerged for the spontaneous assembly of empty capsids [10][11][12][12][13][14][15]21,26,28,[47][48][49][50][51][52][53]. Assembly occurs through a sequential addition process in which individual subunits or larger intermediates [26,52] bind to a growing capsid.…”
Section: Introductionmentioning
confidence: 99%
“…Several theoretical models have explored the underlying mechanism of virus capsid assembly (29,(34)(35)(36)(37)(38)(39)52). Most models strictly impose spherical geometry and/or icosahedral symmetry at all times, and the simplest models generate unwanted multiplicity or degeneracy of structures not observed in nature.…”
Section: Relation To Previous Simulation Studies Of Virus Assemblymentioning
confidence: 99%