A computational study on bacterial trigger factor and ribosome dynamics

Abstract

Trigger factor (TF), found in bacterial cells and chloroplasts, is the first chaperone that welcomes the newly synthesized nascent polypeptide chains to acquire their native fold. In this thesis, four independent 200 ns long molecular dynamics (MD) simulations were performed in explicit solvent at different ionic strengths (29 mM, 50 mM and two simulations for 150 mM). Root mean square deviations from initial structure and residue mean square fluctuations from the average structure indicated high conformational flexibility of TF. Large oscillations in gyration radius were also observed, but a fully collapsed state reported recently was not detected. A unique coil to helix formation in the binding loop took place during 29 mM run. Principal component analysis of MD trajectories and anisotropic network modelling (ANM) calculations were carried out to reveal the collective dynamics of apo TF. Domain decompositions within TF obtained from both of these methods were consistent. In the first collective mode, there is generally an anti-correlated motion between the three major domains, namely binding (BD), core (CD) and head (HD) domains. HD motion with respect to CD is more dominant at 150 mM ionic strength, however opening/closing between BD-CD and CD-HD appear at the same time at 29 mM and 50 mM runs. All snapshots from four simulations were clustered after performing overall alignment and domain-wise alignment. Resulting clusters further elucidated the inter-domain and intra-domain conformational changes. Dynamics of TF-ribosome complex were investigated after docking centroids from major clusters of apo TF runs on to a fragment of BD that was co-crystallized with ribosome 50S subunit. ANM was applied on eight different ribosome 50S-docked TF complexes. The collective dynamics were modified upon complex formation depending on the conformation and position of TF docked on 50S. For most docked conformers, HD was larger compared to apo TF, moving again in an anti-correlated manner with respect to BD and CD. In two of the docked conformers, TF moved as a fully correlated entity on 50S. Distribution of total solvent accessiable surface values calculated for all structure was similar to the distribution of gyration radii.