Figure 6.
Flexibility characterization of DENV-2 NS2B18NS3, showing an ensemble of seven possible positions for the protease domain based on EOM 2.0 analysis. (a) Different views of the ensemble models in cartoon representation with the helicase domain of DENV-2 NS2B18NS3 in orange and the flexible protease domain in blue, together with their conformational contributions (purple blue, 50%; blue, 8%; light blue, 8%; slate blue, 8%; marine blue, 8%; violet purple, 8%; light purple, 8%; the connecting linkers are rendered semi-transparent and NS2B18 is in green). (b) Comparison between the R g distributions (pool, black; ensemble, red) shows a random flexibility as confirmed by R flex (∼81.5% versus ∼85%, with 85% as the threshold value for randomness) and R σ = 0.89. The R g which corresponds to the DENV-4 NS2B18NS3 crystal structure (PDB entry 2vbc) is labelled with a light blue arrow. (c) SAXS pattern (black circles) and calculated ensemble scattering profiles (red line) with a discrepancy χ2 of 0.157.