Title: Computational Studies to Elucidate the Fundamental Mechanism of
Transcription is the key control step in gene expression. RNA polymerases (RNAP) oscillate at every step of transcription elongation among pre-translocation, post-translocation, and backtracked states. Recently, multiple states of the RNAP have been determined by X-ray crystallography. However, these are only snapshots of the molecule in action. The mechanisms of transitions between the states remain a mystery. We aim to fill the gaps between these X-ray structures and define the entire pathway of the transcription process using simulation tools. First, we perform all-atom molecular dynamics simulations in explicit solvent for the whole transcription complex to study structural basis of transcription fidelity. Our results showed that the force field was accurate enough to model key interactions between the trigger loop (an important motif in RNAP) and NTP, for example that of a Histidine residue in the trigger loop with NTP phosphate, borne out experimentally by point mutagenesis. Second, we develop a Molecular Dynamics Morphing technique to reveal the pathways between the various translocation states. Moreover, Hamiltonian Replica Exchange or Simulated Scaling enhanced sampling methods are proposed to obtain the free energy landscapes associated with the translocation process with morphing constraint potential applying on different replicas.