Fig. 8 | Scientific Reports

Fig. 8

From: Immunoinformatics-based design of a next generation multi-epitope vaccine candidate against Shigella boydii using a hierarchical subtractive proteomics approach

Fig. 8

MD Simulation Analysis of Protein Complex (A) RMSD analysis of Chain A (black) and Chain K (blue) over 100 ns simulation. The plot displays early structural relaxation and subsequent stabilization and this implies that conformational integrity is held over the course of the trajectory. (B) Solvent Accessible Surface Area (SASA) of the protein complex, as a function of time. A significant drop in SASA in the initial stage of the simulation indicates the growing compactness during the attainment of equilibrium in the system. (C) Root Mean Square Fluctuation (RMSF) of Chain K, where localized flexibility and regions of dynamism in a sequence can be seen. (D) Root Mean Square Fluctuation (RMSF) per residue of the Chain A where there is fluctuation in the mobility of the atom and the rigid or flexible part of the chain is indicated. (E) Radius of gyration of the protein complex over simulation time span. The trajectory also shows that overall compactness and tertiary structure is retained, with no signs of unfolding.

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