Mechanical stability analysis.

<p>(a) Optical tweezers setup (b) Force-extension curve of dsDNA showing overstretching at 65 pN, as well as the characteristic step-wise relaxation. The measured DNA stretching curves did not display additional steps that might have arisen from STN unfolding or its detachment from the surface. (c) Fraction of tethers that resisted 60 pN in first and second pull, compared between several commonly used linkage strategies and our proposed linkage strategies based on STN. For the (STN)biotin-DNA-Dig(AntiDig) system, almost all tethers broke at the first pull, and hence the subsequent pulls are not indicated.</p

Structural view of hydrophobicity in Trigger factor.

<p>(<b>A</b>) Surface of Trigger factor colour-coded according to the red-white-green (RWG) hydrophobicity scale for the extended conformation. (<b>B</b>) Cartoon representation of Trigger factor with bead-representation (RWG hydrophobicity scale for extended conformation) for the residues involved in inter-domain interactions responsible for stabilisation of the “collapsed” conformation. (<b>C</b>) Cartoon representation of Trigger factor’s collapsed conformation with interacting residues represented as beads (RWG hydrophobicity scale for collapsed conformation). (<b>D</b>) Surface of Trigger factor (collapsed conformation) colour-coded according to the RWG hydrophobicity scale for collapsed conformation.</p

Cartoon representation of the folding of MBP in complex with TF.

<p>For each folding stage, a representative snapshot is shown, with MBP (and its partial folds) in pale red and TF in cyan. The schematic shows a series of events in the cycle, which starts with the interactions between folding intermediates of substrate proteins (MBP in this case) with TF and results in the fully folded substrate protein released from the TF at the end. This may involve more than one TF molecules.</p

Four 200 ns long AA-MD simulations of extended TF each with full MBP and P2.

<p><b>A.</b> Contact probabilities of TF residues with MBP (top panel) and P2 (bottom panel). The barcode plots the standard hydrophobicity map of TF: color-scaled from red (hydrophilic) to green (hydrophobic). <b>B.</b> Distribution of the fraction of hydrophilic contacts in TF-substrate binding for different substrates. The dashed lines plot the distribution in the first 10 ns, while solid lines with circles plot the distribution over the whole trajectory. <b>C.</b> Visualization of the most important interaction sites (blue) on TF for MBP and P2. <b>D.</b> Representative final conformations of TF-MBP and TF-P2 complexes. The substrates are shown in transparent white colored wire-mesh.</p

Steady-state probability distribution of the growth rate for the three IPTG concentrations: Low (black), intermediate (red), high (blue).

<p>Steady-state probability distribution of the growth rate for the three IPTG concentrations: Low (black), intermediate (red), high (blue).</p

Pedigree tree representing the evolution of the colony of <i>E. coli</i>. studied in Ref. [4].

<p>The splitting of the branches corresponds to cell division events, each colored point is associated to a measurement of a single cell and the colors represent the growth rates as shown in the bar in the lower part of the figure.</p

Theoretical values of in the original model of Ref. [4].

<p>Theoretical values of in the original model of Ref. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187431#pone.0187431.ref004" target="_blank">4</a>].</p

Contacts between N-terminal and Arm2.

<p>List of amino-acid residue pairs involved in inter-domain interactions between N-terminal and Arm2, arranged in descending order of occurrence. Contacts expected to be hydrophobic are italicised.</p

Flexibility of Trigger factor.

<p>(<b>A</b>) Crystal structure of Trigger factor monomer (1W26): N-terminal is shown in blue; PPIase domain (Head) shown in red; C-terminal is shown in yellow, with the two arm-like extensions – Arm1 and Arm2 - shown in orange and green respectively. The long helix connecting head and arm1 is shown in yellow and named Head-Arm1 linker. The signature motif that binds TF to the ribosome is illustrated in green beads <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059683#pone.0059683-Hoffmann1" target="_blank">[11]</a>; (<b>B</b>) The 3 resulting structures corresponding to the 3 representative trajectories (same colour coding as (A)), obtained after 250 ns long simulations; (<b>C</b>) Structural deviations of Trigger factor over time are quantified through average root-mean square deviations (RMSD) of C- atoms from their respective positions in the crystal structure. The plot shows 3 representative RMSD time evolutions: represents 6 trajectories with significant deviations from the crystal structure, is representative of 5 trajectories with the least deviations from the crystal structure, while represents 1 trajectory with the highest deformation; (<b>D</b>) Time-averaged root mean square fluctuations (RMSF) plotted for each amino acid residue. The solid lines represent the fluctuations over the complete trajectory, while the dashed lines represent the structural fluctuations in the last 20 ns of the respective trajectories. Graphs , and are averaged over the trajectories that they represent. The secondary structure elements corresponding to the residues are plotted on the bottom x-axis: indigo blocks represent -helices, ocher blocks -strands, and red blocks helices. The tertiary structure is represented at the top x-axis as blocks that colour-coded in the same way as in (A).</p

Comparisons between MD simulations of folded P1 with TF in Touching Complex (TC), and Hugging Complexes (HCs).

<p><b>A.</b> Contact probabilities of TF residues with P1 in four TF-P1 Touching and Hugging Complexes. The barcode plots the hydrophobicity map of TF: color-scaled from red (hydrophilic) to green (hydrophobic). <b>B.</b> Corresponding contact probabilities of P1 residues with TF plotted in the same order of panels. The secondary structure of P1 is represented on the x-axis: orange regions for <i>β</i>–strands, indigo for <i>α</i>–helices, iceblue for turns, dark blue for bends, and the rest represents coils. <b>C.</b> Distributions of the number of intact PF-contacts in folded P1. <b>D.</b> Distributions of the number of TF-P1 contacts (left panel) and TF-P1 COM distance (right panel), in Touching Complexes(black lines) and Hugging Complexes (blue lines), respectively. <b>E.</b> Visualization of the interaction sites on TF’s surface the P1 in the TC, colored from red (least likely) to blue (most likely). <b>F.</b> Representative final TC conformation, with P1 shown in transparent white colored wire-mesh. <b>G.</b> Representative final HC conformation.</p