Mizrahi I, Bruinsma R, Rudnick J. Spanning tree model and the assembly kinetics of RNA viruses.
Phys Rev E 2022;
106:044405. [PMID:
36397584 DOI:
10.1103/physreve.106.044405]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/17/2022] [Indexed: 06/16/2023]
Abstract
Single-stranded RNA (ssRNA) viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization. However, during the self-assembly of complete viral particles in the cytoplasm of an infected cell, the viral genome molecules must be selected from a large pool of very similar host messenger RNA molecules and it is not known whether this also can be understood by free energy minimization. We address this question using a simple mathematical model, the spanning tree model, that was recently proposed for the assembly of small ssRNA viruses. We present a statistical physics analysis of the properties of this model. RNA selection takes place via a kinetic mechanism that operates during the formation of the nucleation complex and that is related to Hopfield kinetic proofreading.
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