Computer simulations show that liquid-liquid phase separation enhances self-assembly
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arXiv
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| Main Authors: | , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866908365493370880 |
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| author | Frechette, Layne B. Sundararajan, Naren Caballero, Fernando Trubiano, Anthony Hagan, Michael F. |
| author_facet | Frechette, Layne B. Sundararajan, Naren Caballero, Fernando Trubiano, Anthony Hagan, Michael F. |
| contents | Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them, including self-assembly reactions. For example, it has been shown that many viruses form condensates within their host cells to compartmentalize capsid assembly and packaging of the viral genome. Yet, the physical principles controlling condensate-mediated self-assembly remain incompletely understood. In this article we use coarse-grained molecular dynamics simulations to study the effect of a condensate on the assembly of icosahedral capsids. The capsid subunits are represented by simple shape-based models to enable simulating a wide range of length and time scales, while the condensate is modeled implicitly to study the effects of phase separation independent of the molecular details of biomolecular condensates. Our results show that condensates can significantly enhance assembly rates, yields, and robustness to parameter variations, consistent with previous theoretical predictions. However, extending beyond those predictions, the computational models also show that excluded volume enables control over the number of capsids that assemble within condensates. Moreover, long-lived aberrant off-pathway assembly intermediates can suppress yields within condensates. In addition to elucidating condensate-mediated assembly of viruses and other biological structures, these results may guide the use of condensates as a generic route to enhance and control self-assembly in human-engineered systems. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_10400 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Computer simulations show that liquid-liquid phase separation enhances self-assembly Frechette, Layne B. Sundararajan, Naren Caballero, Fernando Trubiano, Anthony Hagan, Michael F. Soft Condensed Matter Statistical Mechanics Biological Physics Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them, including self-assembly reactions. For example, it has been shown that many viruses form condensates within their host cells to compartmentalize capsid assembly and packaging of the viral genome. Yet, the physical principles controlling condensate-mediated self-assembly remain incompletely understood. In this article we use coarse-grained molecular dynamics simulations to study the effect of a condensate on the assembly of icosahedral capsids. The capsid subunits are represented by simple shape-based models to enable simulating a wide range of length and time scales, while the condensate is modeled implicitly to study the effects of phase separation independent of the molecular details of biomolecular condensates. Our results show that condensates can significantly enhance assembly rates, yields, and robustness to parameter variations, consistent with previous theoretical predictions. However, extending beyond those predictions, the computational models also show that excluded volume enables control over the number of capsids that assemble within condensates. Moreover, long-lived aberrant off-pathway assembly intermediates can suppress yields within condensates. In addition to elucidating condensate-mediated assembly of viruses and other biological structures, these results may guide the use of condensates as a generic route to enhance and control self-assembly in human-engineered systems. |
| title | Computer simulations show that liquid-liquid phase separation enhances self-assembly |
| topic | Soft Condensed Matter Statistical Mechanics Biological Physics |
| url | https://arxiv.org/abs/2505.10400 |