Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hen...

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Bibliographic Details
Published in:PLoS computational biology 2013-11, Vol.9 (11), p.e1003331-e1003331
Main Authors: Polles, Guido, Indelicato, Giuliana, Potestio, Raffaello, Cermelli, Paolo, Twarock, Reidun, Micheletti, Cristian
Format: Article
Language:English
Subjects:
Capsid - chemistry
Capsid - metabolism
Capsid Proteins - chemistry
Capsid Proteins - metabolism
Cell cycle
Computational biology
Computer Simulation
Crystal structure
Decomposition
Experiments
Mechanics
Models, Molecular
Proteins
Reproducibility of Results
Viruses
Viruses - chemistry
Viruses - metabolism
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Summary:Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1003331