An in silico study on ribosome-binding trigger factor

Abstract

The trigger factor protein (TF), unique to bacterial organisms, binds to ribosome tunnel mouth and works as a chaperone in helping the nascent chains emerging from the ribosome tunnel to acquire their native fold. A 500 ns molecular dynamics (MD) simulation of apo TF was performed in this thesis in order to investigate its structure-dynamics-function relationship, which has not been reported before. Deviations from the initial structure and residue fluctuations point to high mobility and flexibility of TF. Snaphots from the trajectory were aligned onto the crystallized structures of TF binding domain on the ribosome; in this way, novel ribosome-bound conformations for TF were proposed and their compatibility with TF function was assessed. Also, TF electrostatics were elucidated using the Adaptive Poisson-Boltzmann Solver (APBS) program, which reveal enrichment of GLU and LYS residues on TF surface and positive charge distribution of binding region. Essential dynamics of the MD trajectory elucidated the opening up/closing cycle of TF molecule's head and binding domains that may be important for its interaction with the nascent chain. Anisotropic network modelling (ANM) calculations also provided consistent collective modes with the essential dynamics obtained from MD. As a result, TF’s inter-domain movements were uncovered and conformations of full length TF aligned on ribosome tunnel were proposed in this thesis.