Evaluating the Structural Stability of Hen Egg- White Lysozyme (HEWL) in Short-Term Molecular Dynamics Simulation
Abstract
Background: Molecular dynamics (MD) simulations offer a practical computational method to examine protein flexibility and stability at an atomic level under physiological conditions. In structural biology, hen egg-white lysozyme (HEWL), a globular protein of known structure with 129 residues, serves as an excellent model system because it has a compact fold and a large body of experimental data.
Aim: This study aimed to evaluate the dynamic structural stability of HEWL through a 5 ns MD simulation, with focused analysis on the initial 60 ps segment using the AMBER99SB force field and the SPC/E water model.
Methods: The simulation procedure involved energy minimization, equilibration and production run. The major structural descriptors, namely root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) were evaluated using GROMACS tools, whereas the results of conformational changes were graphically illustrated by superimposing selected frames from the simulation trajectory.
Results: The outcomes demonstrated a very stable backbone composition: RMSD stayed at ~0.015 nm, indicating minimal backbone movement; RMSF remained within the range of 0.012- 0.020 nm and indicating low residue-level fluctuation, and the radius of gyration dispersed very little (1.395- 1.402 nm), confirming persistent structural compactness. The structural overlays of the first and last frames also reinforced the numerical data since it indicated a well conserved fold with slight local deviations.
Conclusions: HEWL retains its native structure under the simulation parameters, reinforcing its status as a model protein in MD-based structural studies which involve short-timescale simulations to capture the key dynamics.
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