Molecular dynamics of a protein with cysteine coordinated Zn.

Molecular dynamics simulation of a protein/zinc complex. This was performed with the AMBER forcefield using the GROMACS suite. Amber allows for the use of deprotonated cysteine residues crucial for zinc binding.
Notice the two water molecules that remained close to the cysteine residues throughout the 2 ns of the simulation.
Simulations run in the absence of the Zn ion lead to the unfolding of the region where its suppose to bind.

Visualization was done with VMD.

Category:

Science & Technology

Tags:

• Molecular Dynamics
• Amber
• Gromacs
• Zinc
• deprotonated cysteines.

[wolfgangouille]

Awesome.