Structural analysis of antigenic variation and adaptive evolution of the H5N1 neuraminidase gene
Fig 5
Molecular Dynamics Equilibration Trajectories for Native and Mutant Neuraminidase 1 (NA1) Constructs.
This figure presents the equilibrium trajectories for the MD simulations of the Native NA1 structure (PDB ID: 2HTY) and the five investigated mutant constructs. Each panel plots the System Density (kg/m3) against the Simulation Time (ns) for the duration of the equilibration phase (1.6 ns). The stability of all trajectories, characterized by minimal fluctuations and the maintenance of a consistent average value over the 1600-time steps, confirms that all simulation systems achieved thermodynamic equilibrium prior to the production runs. This stability is a prerequisite for reliable statistical sampling of the conformational landscape and analysis of dynamic properties. The mutants shown are: K207I, K207H, K207W, E229S, and G324T.