Figure 1. Mapping entropy distribution through the translation elongation cycle: the LSU is activated first, followed by the SSU. Eight different ribosome.

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Figure 1. Mapping entropy distribution through the translation elongation cycle: the LSU is activated first, followed by the SSU. Eight different ribosome complexes were biochemically isolated and characterized by hSHAPE. The hSHAPE data were mapped to the atomic resolution ribosome structure (35) and converted to 3 Å voxels in which red represents volumes of high flexibility, green medium flexibility and white low flexibility. (A) Empty ribosomes. (B) P site occupied (by Ac-PhetRNA<sup>Phe</sup>). (C) Pre-accommodation complex. (D) Classical states complex. (E) Postaccomodation complex. (F) Hybrid states complex. (G) Pre-translocation complex. (H) Posttranslocation complex. In each panel, E denotes the occupancy state of the ribosomal E site, P denotes the P site, A refers to the A site, and F indicates the occupancy status of the elongation factor binding site. Ø indicates that these sites are unoccupied, P/P and AA/ are classical state peptidyl- and aminoacyl-tRNA, respectively, and P/E and A/P denote hybrid state tRNAs. PTC: peptidyltransferase center; DC: decoding center; ASF: A-site finger (H38); head: small subunit head structure. A full rendering of these states in 3D is shown in Supplementary Video 1. From: Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle Nucleic Acids Res. 2017;45(8):4958-4971. doi:10.1093/nar/gkx112 Nucleic Acids Res | © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 2. Intersubunit bridge nucleotides reverse their flexibility patterns as the ribosome progresses from accommodation through translocation. hSHAPE data were applied to the atomic resolution structure of the yeast ribosome, using the color scheme indicated at bottom (described in Supplementary Figure S2) to represent relative changes in the flexibilities of nucleotides participating in the indicated intersubunit bridges. (A) Postaccommodation complex nucleotide flexibility values were compared to those of P site occupied ribosomes. (B) Posttranslocation complex flexibility values were compared to those of the postaccommodation complex. From: Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle Nucleic Acids Res. 2017;45(8):4958-4971. doi:10.1093/nar/gkx112 Nucleic Acids Res | © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 3. Correlated and anti-correlated changes in base flexibility reveal of allosteric communication pathways in elongation factor bound ribosomes. hSHAPE data were analyzed to identify rRNA nucleotides which display similar changes in chemical reactivity with one another through the elongation cycle. These are listed in Supplementary Table S4. These were mapped to the 5.5 Å cryo-EM model of the translating eukaryotic ribosome (99), in which red colored nucleotides show linked loss of flexibility and green nucleotides have linked increased flexibility. The helices in which these nucleotides are located are shown with matching colors or gray for helices harboring both red and green residues. Selected ribosomal proteins are colored light blue. These analyses reveal nucleotides and helices joining the P stalk base (H42–43) with the following. (A) The PTC, tRNA binding sites (A, P, E). (B) The PTC, SRL, intersubunit bridges B6, eB11, eB13. (C) Intersubunit bridge B7b/c. (D) Expansion segment 7L, the PTC, 5.8S, LSU Domain III (H47–59), and expansion segment 27L. Taken as a whole, two different possible allosteric communication pathways are mapped. (E) One extending from the elongation factor binding site (EF) to the PTC from where it branches out to the tRNA binding pockets, to ES27L through Domain III (H47–59), or to the small subunit through bridge B7b/c. (F) A second network maps from the elongation factor binding site to the small subunit through intersubunit bridges B1b/c, B6, eB11 and eB13. From: Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle Nucleic Acids Res. 2017;45(8):4958-4971. doi:10.1093/nar/gkx112 Nucleic Acids Res | © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 4. The pre-translocation ribosomal complex RNAs colored according to the log-normalized SHAPE reactivity computed from simulation and measured by experiments. Reactivity of each nucleobase is computed from the angle fluctuations between the two consecutive bases using all atom molecular dynamics simulations. Proteins that are included in the simulations are omitted for clarity. (A) The computed reactivity using the standard potential energy function. (B) Result of computed reactivity after forcefield parameters were optimized based on experimental SHAPE data using SHAPE-FIT method. (C) hSHAPE reactivity from the experiments for comparison. (D) Base by base comparison of computed and measured SHAPE reactivity of 80S empty ribosome RNAs after the forcefield parameters were optimized using SHAPE. From: Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle Nucleic Acids Res. 2017;45(8):4958-4971. doi:10.1093/nar/gkx112 Nucleic Acids Res | © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com