The Genesis of Ribosome Structure: How a Protein Generates RNA Structure in Real Time

Deletion of L4 domains reveals insights into the importance of ribosomal protein extensions in eukaryotic ribosome assembly

“…Therefore, it has been hypothesized that r-proteins participate in the dynamic folding and stabilization of rRNA during ribosome assembly and function (Klein et al 2004). This has been supported by thermodynamic and kinetic studies on in vitro reconstitution of bacterial ribosomes (Recht and Williamson 2004;Holmes and Culver 2005;Ramaswamy and Woodson 2009a,b;Woolstenhulme and Hill 2009;Calidas and Culver 2010;Mayerle and Woodson 2013). In eukaryotes, conserved r-proteins have also evolved extra amino acid sequences that are largely found in either carboxy-or amino-terminal domains Yusupova and Yusupov 2014).…”

The Formation of a Potential Spring in the Ribosome

“…Using more physiological conditions (Mg 2+ ∼ 3-10 mM), other studies have shown that substantial changes in the global structure of rRNA occur upon the addition of proteins to rRNA. 8,10,[14][15][16][17]19,[25][26][27][28][29][30] Our results, obtained under more physiological Mg 2+ concentrations (≤ 10 mM), show that the ribosomal proteins are perpetrators of a significant amount of very specific rRNA folding. For instance, we previously have shown that the kink-turn found in the 280 region of 16S rRNA in the crystal structure was actually formed in a sequential time-dependent manner as protein S17 was bound to the 16S rRNA.…”

“…Initial studies of protein S17 binding to 16S rRNA showed that base C264 was protected from methylation by DMS as protein S17 was bound. 17 DMS methylates N 1 of A, N 3 of C and N 7 of G if those atoms are accessible to the solvent. By analyzing the crystal structure of this region, 4 it can be seen that Arg64 and Pro65 of protein S17 have van der Waals contacts with C264.…”

“…We previously found that as protein S17 binds to 16S rRNA, the binding is very specific, with the protein seeking out specific structured regions of the naked rRNA. 17 In the process of binding, a basic ribosomal protein generally binds to specific structured regions of the acidic rRNA. The neutralizing effect of the protein affects regions of rRNA proximal to the binding region of the protein, inducing structural changes in these adjacent regions.…”

“…An example of this is the discovery of the formation and buttressing of the kink-turn between bases G278 and C280 as protein S17 is bound to the 269-273 region of helix 11 in16S rRNA. 17 The present study was designed to understand the structural deformations occurring in a small region of the ribosome during the assembly process. In turn, we have tried to understand the role of this region in the mechanistic process carried out by the ribosome during protein biosynthesis.…”