Figure 5
The residue fluctuations, transitions and short transitions of selected regions of T7RNAP calculated using T-pad tool and plotted based on the residue and their PAD degree from 100 ns MD simulation. The local fluctuations identified from the regions with high RMSF at pH 5 were shown for (a) N-terminal and (b) Thumb sub-domain and (c) finger sub-domain. The plots: (d,e and f) shows local fluctuations in the residues in vicinity of active site region at, pH 5, neutral pH and pH 7.9 respectively.
