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变形病毒衣壳的分子动力学模拟。

Molecular Dynamics Simulations of Deformable Viral Capsomers.

机构信息

Intelligent Systems Engineering, Indiana University, Bloomington, IN 47408, USA.

出版信息

Viruses. 2023 Jul 31;15(8):1672. doi: 10.3390/v15081672.


DOI:10.3390/v15081672
PMID:37632014
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10459744/
Abstract

Most coarse-grained models of individual capsomers associated with viruses employ rigid building blocks that do not exhibit shape adaptation during self-assembly. We develop a coarse-grained general model of viral capsomers that incorporates their stretching and bending energies while retaining many features of the rigid-body models, including an overall trapezoidal shape with attractive interaction sites embedded in the lateral walls to favor icosahedral capsid assembly. Molecular dynamics simulations of deformable capsomers reproduce the rich self-assembly behavior associated with a general T=1 icosahedral virus system in the absence of a genome. Transitions from non-assembled configurations to icosahedral capsids to kinetically-trapped malformed structures are observed as the steric attraction between capsomers is increased. An assembly diagram in the space of capsomer-capsomer steric attraction and capsomer deformability reveals that assembling capsomers of higher deformability into capsids requires increasingly large steric attraction between capsomers. Increasing capsomer deformability can reverse incorrect capsomer-capsomer binding, facilitating transitions from malformed structures to symmetric capsids; however, making capsomers too soft inhibits assembly and yields fluid-like structures.

摘要

大多数与病毒相关的个体衣壳粒的粗粒化模型都采用刚性构建块,在自组装过程中不表现出形状适应性。我们开发了一种包含衣壳粒拉伸和弯曲能量的粗粒化通用模型,同时保留了刚体模型的许多特征,包括整体梯形形状和嵌入在侧壁中的有吸引力的相互作用位点,以有利于二十面体衣壳的组装。可变形衣壳粒的分子动力学模拟在没有基因组的情况下再现了与一般 T=1 二十面体病毒系统相关的丰富自组装行为。随着衣壳粒之间的位阻吸引力的增加,观察到从非组装构型到二十面体衣壳到动力学捕获的畸形结构的转变。衣壳粒-衣壳粒位阻吸引力和衣壳粒可变形性空间中的组装图表明,将具有更高可变形性的衣壳粒组装成衣壳需要衣壳粒之间的位阻吸引力越来越大。增加衣壳粒的可变形性可以逆转错误的衣壳粒-衣壳粒结合,促进从畸形结构到对称衣壳的转变;然而,使衣壳粒过于柔软会抑制组装并产生类似流体的结构。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/18d758c22e26/viruses-15-01672-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/b9bbf1452e85/viruses-15-01672-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/2bb89ae9b742/viruses-15-01672-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/a931ba245b39/viruses-15-01672-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/db1ceca89c02/viruses-15-01672-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/55cdee83d164/viruses-15-01672-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/18d758c22e26/viruses-15-01672-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/b9bbf1452e85/viruses-15-01672-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/2bb89ae9b742/viruses-15-01672-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/a931ba245b39/viruses-15-01672-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/db1ceca89c02/viruses-15-01672-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/55cdee83d164/viruses-15-01672-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d828/10459744/18d758c22e26/viruses-15-01672-g006.jpg

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本文引用的文献

[1]
Understanding Virus Structure and Dynamics through Molecular Simulations.

J Chem Theory Comput. 2023-6-13

[2]
Essay: Collections of Deformable Particles Present Exciting Challenges for Soft Matter and Biological Physics.

Phys Rev Lett. 2023-3-31

[3]
Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism.

ACS Nano. 2022-9-27

[4]
The Dynamics of Viruslike Capsid Assembly and Disassembly.

J Am Chem Soc. 2022-7-20

[5]
Designing Surface Charge Patterns for Shape Control of Deformable Nanoparticles.

Phys Rev Lett. 2020-12-11

[6]
Computational studies of shape control of charged deformable nanocontainers.

J Mater Chem B. 2019-10-23

[7]
All-atom virus simulations.

Curr Opin Virol. 2018-9-1

[8]
Molecular dynamics study of T = 3 capsid assembly.

J Biol Phys. 2018-6

[9]
Self-assembly of model proteins into virus capsids.

J Phys Condens Matter. 2017-11-29

[10]
Assembled viral-like nanoparticles from elastic capsomers and polyion.

J Chem Phys. 2017-4-7

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