dorsal/arxiv
View SchemaStochastic kinetics of viral capsid assembly based on detailed protein structures
| Authors | Martin Hemberg, Sophia N. Yaliraki, Mauricio Barahona |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0610052 |
| URL | https://arxiv.org/abs/q-bio/0610052 |
| DOI | 10.1529/biophysj.105.076737 |
| Journal | Biophysical Journal Volume 90 May 2006 3029-3042 |
Abstract
We present a generic computational framework for the simulation of viral capsid assembly which is quantitative and specific. Starting from PDB files containing atomic coordinates, the algorithm builds a coarse grained description of protein oligomers based on graph rigidity. These reduced protein descriptions are used in an extended Gillespie algorithm to investigate the stochastic kinetics of the assembly process. The association rates are obtained from a diffusive Smoluchowski equation for rapid coagulation, modified to account for water shielding and protein structure. The dissociation rates are derived by interpreting the splitting of oligomers as a process of graph partitioning akin to the escape from a multidimensional well. This modular framework is quantitative yet computationally tractable, with a small number of physically motivated parameters. The methodology is illustrated using two different viruses which are shown to follow quantitatively different assembly pathways. We also show how in this model the quasi-stationary kinetics of assembly can be described as a Markovian cascading process in which only a few intermediates and a small proportion of pathways are present. The observed pathways and intermediates can be related a posteriori to structural and energetic properties of the capsid oligomers.
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"abstract": "We present a generic computational framework for the simulation of viral\ncapsid assembly which is quantitative and specific. Starting from PDB files\ncontaining atomic coordinates, the algorithm builds a coarse grained\ndescription of protein oligomers based on graph rigidity. These reduced protein\ndescriptions are used in an extended Gillespie algorithm to investigate the\nstochastic kinetics of the assembly process. The association rates are obtained\nfrom a diffusive Smoluchowski equation for rapid coagulation, modified to\naccount for water shielding and protein structure. The dissociation rates are\nderived by interpreting the splitting of oligomers as a process of graph\npartitioning akin to the escape from a multidimensional well. This modular\nframework is quantitative yet computationally tractable, with a small number of\nphysically motivated parameters. The methodology is illustrated using two\ndifferent viruses which are shown to follow quantitatively different assembly\npathways. We also show how in this model the quasi-stationary kinetics of\nassembly can be described as a Markovian cascading process in which only a few\nintermediates and a small proportion of pathways are present. The observed\npathways and intermediates can be related a posteriori to structural and\nenergetic properties of the capsid oligomers.",
"arxiv_id": "q-bio/0610052",
"authors": [
"Martin Hemberg",
"Sophia N. Yaliraki",
"Mauricio Barahona"
],
"categories": [
"q-bio.QM",
"q-bio.BM"
],
"doi": "10.1529/biophysj.105.076737",
"journal_ref": "Biophysical Journal Volume 90 May 2006 3029-3042",
"title": "Stochastic kinetics of viral capsid assembly based on detailed protein structures",
"url": "https://arxiv.org/abs/q-bio/0610052"
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