Comparative Modeling of the Three-Dimensional Structure of Signal Recognition Particle RNA

Comparative sequence analysis and ERNA-3D software were used to model the three-dimensional structures of several signal recognition particle RNAs. RNA secondary structures were established by allowing only phylogenetically-supported base pairs. The folding of the RNA molecules was constrained further to include a pseudoknot and a tertiary interaction. Founded by the concept that all SRP RNAs must be shaped similarly in three dimensions, helical sections were oriented coaxially where a continuous helical stack was formed in the RNA of another species. Finally, RNA helices were placed at distances that preserved the connectivity of the molecule with the smallest number of single-stranded nucleotide residues as identified from the aligned sequences. Representative models of the three-dimensional structures of an eukaryote, an archaeon, and three bacterial SRP RNAs are presented.