Protein-guided RNA dynamics during early ribosome assembly

 

To our knowledge, this collaboration between CPLC faculty Ha and Luthey-Schulten with Woodson at Johns Hopkins presents the first use of single molecule spectroscopy and all-atom simulations to obtain the frequency and direction of helix motions (not only populations) in a large RNA-protein complex. The first proteins to bind the RNA change the rRNA structure in a way that makes it easier for later proteins to join.  How ribosomal proteins recognize the RNA and change its structure so that other proteins can bind is not known. To address this gap, we used two and three-color single molecule FRET and molecular dynamics simulations to observe encounters between E. coli protein S4 and the 5’ domain of 16S rRNA in real time with precision and clarity unprecedented for any RNA-protein complexes. S4 is one of the first proteins to bind the 16S rRNA, and is needed to nucleate 30S ribosome assembly and for the fidelity of translation. At first, the S4-rRNA complex is dynamic and samples many structures, but after a few seconds, it converts to stable complexes that flip between two structures, a native structure and a non-native intermediate. Unexpectedly, nearly all successful S4 binding trajectories pass through the non-native intermediate, contradicting the usual assumption that proteins prefer to bind the natively folded RNA.

Nature, 2014, in press