  The cowpea chlorotic mottle virus (CCMV) has emerged as an exemplary model
system to assess the balance between electrostatic and topological features of
ssRNA viruses, specifically in the context of the viral self-assembly process.
Yet, in spite of its biophysical significance, little structural data of the
RNA content of the CCMV virion is currently available. Here, the conformational
dynamics of the RNA2 fragment of CCMV was assessed via coarse-grained molecular
dynamics simulations, employing the oxRNA2 model. The behavior of RNA2 has been
characterized both as a freely-folding molecule and within a mean-field
depiction of a CCMV-like capsid. For the latter, a multi-scale approach was
employed, to derive a radial potential profile of the viral cavity, from
atomistic structures of the CCMV capsid in solution. The conformational
ensembles of the encapsidated RNA2 were significantly altered with respect to
the freely-folding counterparts, as shown by the emergence of long-range motifs
and pseudoknots in the former case. Finally, the role of the N-terminal tails
of the CCMV subunits (and ionic shells thereof) is highlighted as a critical
feature in the construction of a proper electrostatic model of the CCMV capsid.
