S15 structural variations during MD simulation.

<p>Backbone snapshots of both proteins are in shades of blue (<i>E. coli</i> light blue; <i>T. thermophilus</i> dark blue). Backbone starting structures are shown in yellow.</p

S17 structural variations during MD simulation.

<p>Backbone snapshots of both proteins are in shades of green (<i>E. coli</i> light green; <i>T. thermophilus</i> dark green). Backbone starting structures are shown in yellow.</p

Comparisons of S15, S17, and S20 proteins from two different species.

<p><i>E. coli</i> proteins are shown in the lighter shade and <i>T. thermophilus</i> in the darker shade. Contact residues are shown as stick representations and some important parts of the proteins, discussed in the text, are labeled.</p

Net charges of r-proteins.

<p>Note: S21 for <i>T. Thermophilus</i> is called THX.</p

RMSD values for S15, S17, and S20 proteins.

<p><i>E. coli</i> proteins are represented by lighter squares and <i>T. thermophilus</i> by darker triangles. The S17 include the RMSD value for just the part of the structure that is homologous (dark green) to <i>E. coli</i> S17 (omitting the extra <i>T. thermophilus</i> C-terminal part). Notably, this C-terminal part of S17 causes the <i>T. thermophilus</i> to greatly increase its overall mobility.</p

Contacts between r-proteins and r-RNA in total and for charged residues.

<p>Note: The total number of protein contacts for S15, S17, and S20 above differs from the total number of contact residues presented in Supplementary <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002530#pcbi.1002530.s001" target="_blank">Tables S1</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002530#pcbi.1002530.s002" target="_blank">S2</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002530#pcbi.1002530.s003" target="_blank">S3</a> because some protein residues are in contact with more than one nucleotide, which are presented here as multiple contacts.</p

ANM enrichment factors and significance for 30S proteins.

<p>Note: EF is the enrichment factor, defined as the ratio of root mean square fluctuations for contacting over non-contacting residues. The P-value is the statistical significance computed with a permutation test. See text for details.</p

S20 structural variations during MD simulation.

<p>Backbone snapshots of both proteins are shown in shades of red (<i>E. coli</i> light red; <i>T. thermophilus</i> dark red). Backbone starting structures are in yellow.</p

The 30S <i>T. thermophilus</i> subunit (1J5E), interface side.

<p>The 16S rRNA and r-proteins of interested are highlighted: 5′ Domain yellow, Central Domain grey, 3′ Major Domain orange, and 3′ Minor Domain purple; S15 blue, S17 dark green, and S20 dark red. The <i>E. coli</i> structure (2AVY) is nearly identical, but slight structural differences for the proteins of interest are discussed in the text and visualized in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002530#pcbi-1002530-g002" target="_blank">Figure 2</a>. The remaining r-proteins have been removed for better visualization of the 16S rRNA domains.</p

Average MD RMSF values (in Å; standard deviations in parentheses) and enrichment factors EF.

<p>Average MD RMSF values (in Å; standard deviations in parentheses) and enrichment factors EF.</p