Impact of the RNA Binding Domain Localization of the Protein Shell on Virus Particle Stability
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| Main Authors: | , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866915118303936512 |
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| author | Safdari, Mohammadamin Li, Siyu Panahandeh, Sanaz van der Schoot, Paul Zandi, Roya |
| author_facet | Safdari, Mohammadamin Li, Siyu Panahandeh, Sanaz van der Schoot, Paul Zandi, Roya |
| contents | The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat proteins and the negatively charged polyanions. Theoretically, this interaction is often modeled by coarse-graining the charge distribution of the binding domains, either by projecting the charges onto the inner surface of the protein shell or by spreading them across a region representing the capsid lumen where the binding domains are located. In practice, however, the positive charges are not uniformly distributed across the binding domains, which themselves are positioned at discrete, specific sites on the shell surface. Here, we use molecular dynamics simulations to investigate the impact of localized interactions on the most probable or optimal length of the encapsulated polymer, revealing that the specific location of charges along the binding domains plays a significant role, consistent with experimental observations. Comparing the simulations with predictions from a simple mean-field theory taken from the literature, we find that while the general trends are reasonably well captured, quantitative discrepancies arise between the two approaches. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2501_13891 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Impact of the RNA Binding Domain Localization of the Protein Shell on Virus Particle Stability Safdari, Mohammadamin Li, Siyu Panahandeh, Sanaz van der Schoot, Paul Zandi, Roya Biological Physics The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat proteins and the negatively charged polyanions. Theoretically, this interaction is often modeled by coarse-graining the charge distribution of the binding domains, either by projecting the charges onto the inner surface of the protein shell or by spreading them across a region representing the capsid lumen where the binding domains are located. In practice, however, the positive charges are not uniformly distributed across the binding domains, which themselves are positioned at discrete, specific sites on the shell surface. Here, we use molecular dynamics simulations to investigate the impact of localized interactions on the most probable or optimal length of the encapsulated polymer, revealing that the specific location of charges along the binding domains plays a significant role, consistent with experimental observations. Comparing the simulations with predictions from a simple mean-field theory taken from the literature, we find that while the general trends are reasonably well captured, quantitative discrepancies arise between the two approaches. |
| title | Impact of the RNA Binding Domain Localization of the Protein Shell on Virus Particle Stability |
| topic | Biological Physics |
| url | https://arxiv.org/abs/2501.13891 |