The ribosome is of central importance to all known forms of life, yet the molecular mechanisms of translation are still poorly understood. A mechanistic understanding would pave the way for understanding such diverse topics as HIV pseudo-knot mediated frame shifting, action of current anti-ribosomal antibiotics, in vivo RNA conformational changes, and the cooperation of RNA and protein inside the cell. Current mechanistic understanding of translation centers around tRNA dynamics in a static ribosome. Since 1969 it has been hypothesized that the while adding amino acids to the growing polypeptide, the ribosome cycles between """"""""locked"""""""" and """"""""unlocked"""""""" states that have yet to be observed. Recent crystal structures of the 70S ribosome indirectly support this theory: models of mRNA and tRNA motion predict that known mRNA and tRNA movements during translation require a conformational change of the 70S ribosome. A prime candidate for the conformational change has been a reversible RNA folding of the """"""""Switch Helix"""""""" element of the 16S rRNA. Here I propose a novel single-molecule FRET experiment to answer whether or not the switch-helix is the mechanistic basis of the translocation step on the ribosome. Unlike X-ray and cryo-EM methods, single-molecule FRET experiments can view the entire protein synthesis cycle, and the experiment proposed here could easily be transformed into a high-throughput screening assay for novel small-molecule inhibitors of translation. ? ?
