Journal: Scientific Reports

Article Title: A novel mRNA-based multi-epitope vaccine for rabies virus computationally designed via reverse vaccinology and immunoinformatics

doi: 10.1038/s41598-025-16143-w

Figure Lengend Snippet: Molecular dynamics simulation analyses of the TLR4–vaccine complex with 200 ns. This figure illustrates the dynamic and structural behavior of the TLR4–vaccine complex: (A) RMSD shows an initial rise to ~ 0.15 nm, followed by moderate fluctuations and stabilization between 0.10–0.125 nm, indicating structural convergence. (B) RMSF highlights flexible regions near residues 190, 300, and 340, while most residues remain stable (0.04–0.11 nm), reflecting limited local mobility. (C) Radius of Gyration (Rg) decreases from ~ 6.0 nm to below 4.25 nm, suggesting progressive compaction of the complex. (D) SASA stabilizes between 614–634 nm² after an initial peak, indicating consistent solvent exposure and structural folding. (E) Intermolecular Hydrogen Bonds (F) PCA-Based Conformational Landscape of the TLR4–Vaccine complex derived from a 200 ns molecular dynamics simulation of a TLR4–vaccine complex, mapping the system’s conformational states onto the first two principal components (PC1 and PC2), which represent the dominant motions and energetically favorable conformational states.

Article Snippet: To evaluate the dynamic behavior and stability of the docked TLR4–vaccine complex, an explicit all-atom Molecular Dynamics Simulation (MDS) was performed using GROMACS 2023.1 , compiled with CUDA support to leverage GPU acceleration.

Techniques: Solvent, Derivative Assay