Figure 5
A: The ssRNA channel site of the four helicase structures: the Murray Valley Encephalitis helicase is in green color, the Yellow fever helicase is in pink color, the Dengue helicase is in orange color and the Usutu helicase model is colored red. The ssRNA substrate, indicating the nucleic acid binding channel is showing in magenta spacefill representation and the NTP binding site is in the proximity of the ADP molecule, showing in CPK format. B: The energy vs time plot of the full MD simulation of the Usutu helicase model. The 10 ns MD simulation quickly reached equilibrium and remained stable. C: Energy vs time plot of 10 ns MD simulation for each of the two X-ray structures (Murray Valley Encephalitis and Yellow Fever helicases) and the Usutu helicase model in the presence of the ssRNA fragment, borrowed from the Murray Valley Encephalitis structure (id: 2V80). It was demonstrated that the Usutu helicase model + ssRNA complex (yellow) behaved in a way very similar to that of the Murray Valley Encephalitis X-ray structure + ssRNA (blue) and Yellow Fever X-ray structure + ssRNA (magenta) complexes.