Types
The corresponding cysteines CyA-D connect with Fe1-4, respectively.
Here is a final PDB so one can get an orientation on how the various parts link together.
The application of classical molecular dynamics simulations to the study of metalloenzymes has been hampered by the lack of suitable molecular mechanics force field parameters to treat the metal centers within standard biomolecular simulation packages. These parameters cannot be generalized, nor be easily automated, and hence should be obtained for each system separately. Here we present density functional theory calculations on [Fe2S2(SCH3)4]2+/+, [Fe3S4(SCH3)3]+/0 and [Fe4S4(SCH3)4]2+/+ and the derivation of parameters that are compatible with the AMBER force field. Molecular dynamics simulations performed using these parameters on respiratory Complex II of the electron transport chain showed that the reduced clusters are more stabilized by the protein environment, which leads to smaller changes in bond lengths and angles upon reduction. This effect is larger in the smaller ironsulfur cluster, [Fe2S2(SCH3)4]2+/+.
The parameters work provided the following scheme is used:
Names
Types
The corresponding cysteines CyA-D connect with Fe1-4, respectively.
Here is a final PDB so one can get an orientation on how the various parts link together.