Comparative analyses and molecular videography of MD simulations on WT human SOD1

Abstract

Cu/Zn superoxide dismutase (SOD1) is the antioxidant enzyme that catalyses intracellular superoxide radical. In this study, the molecular dynamics (MD) of six wild-type (WT) human (h) SOD1 PDB crystallographs were computed to comparative analyses and visualisations, including a novel method of high-resolution molecular videography. Production MD were computed across variable matrix conditions for 10 ns (0.01 ns resolution), 37 °C and pH 7.4. MD simulations yielded PCA, RMSD, RMSF, SAS, SS bonds, and H bonds analyses. The attached molecular video comprises 20 s of MD footage at 540p/48 Hz resolution featuring 10 ns of computed trajectories. Of PDB IDs 1HL5, 1PU0, 1SPD, 2C9V, and 2V0A, this study determines that 1PU0 should be implemented as the ideal crystallographic template for ongoing computational works on hSOD1.