F. Musiani, G. Rossetti, L. Capece, T. Gerger, C. Micheletti, G. Varani and Po. Carloni
MD simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 TAR RNA
J. Am. Chem. Soc., 2014, 136 , 15631-15637
Link to online article

Abstract
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. In order to further explore the compactness selection hypothesis, we systematically compare the predicted sizes of more than one hundred wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints. In particular, we enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact. It is found that progressive accumulation of these restricted mutations still suffices to completely erase the characteristic compactness imprint of the viral RNA genomes, making them in this respect physically indistinguishable from randomly shuffled RNAs. This shows that maintaining the physical compactness of the genome is indeed a primary factor among ssRNA viruses evolutionary constraints, contributing also to the evidence that synonymous mutations in viral ssRNA genomes are not strictly neutral.