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Molecular Dynamics Simulations

Running computational simulations to visualize how G6PD mutations affect protein stability and dynamics at the atomic level.

Live Simulation Visualization

RMSD: 2.34 Å ▲ 0.02
Temperature: 310 K
H-Bonds: 342 ▼ 3
Time: 45.2 ns
Energy: -45,230 kJ/mol
100
ns Simulation
~8K
Atoms Tracked
2
fs Timestep
50M
Frames

RMSD Over Time

Wild Type
Mediterranean

Root Mean Square Deviation (RMSD) measures how much the protein structure deviates from its starting configuration. Higher values indicate instability.

Hydrogen Bonds

H-bond count

Hydrogen bonds are critical for protein stability. The S188F mutation disrupts key bonds at the dimer interface.

What the Simulations Reveal

40% Higher RMSD in Mutants

Mediterranean variant (S188F) shows significantly higher structural deviation over 100ns, indicating reduced stability compared to wild-type enzyme.

Disrupted Dimer Interface

The S188F mutation breaks critical hydrogen bonds at the dimer interface, weakening the quaternary structure essential for enzyme function.

Weakened NADP+ Binding

Class I mutations show increased flexibility in the NADP+ binding pocket, reducing cofactor affinity critical for enzyme stability.

Flexibility Hotspots Identified

RMSF analysis reveals increased flexibility in catalytically important regions (residues 180-200) in mutant structures.

Tools & Methods

🔬
GROMACS 2023
MD simulation engine
CHARMM36
Force field parameters
🎨
VMD
Visualization software
🐍
MDAnalysis
Python analysis toolkit

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