UNASSIGNED: Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome, capsid and between individual capsid proteins (i.e. "capsid architecture") are intimate and expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification, for @entity8038 making icosahedral virus capsids, is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we have searched for both @entity3689 and @entity4334 sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the Pandoravirus capsid protein. We show that the structure-based classification is strongly supported by @entity3689 and also @entity4334 sequence similarity, suggesting that similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE: Viral capsids protect nucleic acid genomes which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein coding @entity4334 sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detect similarity at @entity4334 level between capsid protein coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids.

Nucleic and XXXX sequences support structure-based viral classification.

@entity4334 :: ('D009711', 'Chemical') :: ['nucleotide'] @entity3689 :: ('D000596', 'Chemical') :: ['amino acid'] @entity8038 :: ('MESH:D058456', 'Disease') :: ['viral coat proteins']
@entity3689 :: (D000596,Chemical) :: ['amino acid']
