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. 2017 Apr 24;12(4):e0176262.
doi: 10.1371/journal.pone.0176262. eCollection 2017.

Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states

Mehmet Tarik Can  1 , Zeynep Kurkcuoglu  1 , Gokce Ezeroglu  1 , Arzu Uyar  1 , Ozge Kurkcuoglu  2 , Pemra Doruker  1
Affiliations

Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states

Mehmet Tarik Can et al. PLoS One. .

Abstract

The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and chloroplasts. In this study, we aim to investigate the functional dynamics of fully-atomistic apo TF and its complex with 50S. As TF accomodates a high percentage of charged residues on its surface, the effect of ionic strength on TF dynamics is assessed here by performing five independent molecular dynamics (MD) simulations (total of 1.3 micro-second duration) at 29 mM and 150 mM ionic strengths. At both concentrations, TF exhibits high inter- and intra-domain flexibility related to its binding (BD), core (CD), and head (HD) domains. Even though large oscillations in gyration radius exist during each run, we do not detect the so-called 'fully collapsed' state with both HD and BD collapsed upon the core. In fact, the extended conformers with relatively open HD and BD are highly populated at the physiological concentration of 150 mM. More importantly, extended TF snapshots stand out in terms of favorable docking onto the 50S subunit. Elastic network modeling (ENM) indicates significant changes in TF's functional dynamics and domain decomposition depending on its conformation and positioning on the 50S. The most dominant slow motions are the lateral sweeping and vertical opening/closing of HD relative to 50S. Finally, our ENM-based efficient technique -ClustENM- is used to sample atomistic conformers starting with an extended TF-50S complex. Specifically, BD and CD motions are restricted near the tunnel exit, while HD is highly mobile. The atomistic conformers generated without an NC are in agreement with the cryo-EM maps available for TF-ribosome-NC complex.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Structure and dynamics of apo TF in solution.
(A) Domains of apo TF and its structural components with head (HD), core (CD) and binding domains (BD), (B) color-coded residue RMSF values sorted from highest (red) to lowest (blue) and (C) Residue RMSF based on domain-wise alignments, for 29 mM and 150 mM ionic strengths. Each domain is distinguished with dashed lines.
Fig 2
Fig 2. Histograms for radius of gyration and inter-domain distances.
(A) Radius of gyration, (B) BD-Arm2 distance, and (C) HD-Arm1 distance for the 29mM (blue) and 150mM (red) runs. All distances cover broad ranges, in conformity with high flexibility of TF. 150 mM snaphots exhibit relatively more extended conformations.
Fig 3
Fig 3. HD-Arm1 distance vs. BD-Arm2 distance plot for three independent runs at 150 mM ionic strength.
Blue diamonds correspond to extended conformers docked onto 50S without clashes. Red squares and spheres are docked conformers with specific clashes, as listed in Table 1.
Fig 4
Fig 4. Residue cross-correlations and harmonic motions for TF structures.
In the left panels, residue cross-correlations are displayed for TF structures in (A) its apo form and (B), (C) two different complexes with 50S, based on 10 slowest ENM modes. Blocks on the maps point to domain decomposition on TF, as shown with different colors on cartoon representations in the middle panels. In the right panels, harmonic motions for the first modes are shown only for TF docked to 50S (gray spheres) from different perspectives, with the same domain coloring.
Fig 5
Fig 5. Atomistic TF-50S conformers from ClustENM fitted into cryo-EM maps.
(A) Starting structure (opaque) and generated conformers (transparent) of TF-50S complex from ClustENM shown for side and top views. TF (orange), 50S (grey) and several ribosomal proteins neighboring TF are explicitly shown. In the bound state on ribosome, CD and BD of TF are almost fixed, whereas HD is highly flexible. HD moves in parallel to the surface of ribosome but also experiences up-down motion (B) Side and top views for three aligned cryo-EM map densities (grey: EMD-1499, pink: EMD-2696, cyan: EMD-2711) using Chimera, revealing the lateral head domain motion of TF in the presence of nascent polypeptide chain. (C) Side and top views for all 17 atomic conformers from ClustENM fitted into superimposed cryo-EM maps in (B) showing good conformity between our ENM calculations and the experimental data.
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The authors received no specific funding for this work.