Physical Sciences and Mathematics Commons^™

Structural And Evolutionary Classification Of G/U Wobble Basepairs In The Ribosome, Neocles B. Leontis, Ali Mokdad, Maryna V. Krasovska, Jiří Sponer

Chemistry Faculty Publications

We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/U shallow groove pocket-like packing interactions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions)-lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved …