Hello everyone, good day!
I'm currently working on a project involving metalloprotein conformational changes induced by the binding of specific metal ions, such as As(III) in the environment where Pb(II) is also present.
I plan to create mutations in the protein, perform energy minimization, and then place the metal ions into the binding pocket, finally by a docking protocol. The goal is to identify the most suitable protein conformation for As(III) binding while minimizing unwanted binding from Pb(II). I planned to choose the construct with the lowest total score when binded to As(III) while achieving the highest score for Pb(II) binding. The binding affinity can later validated through experiments.
Additionally, I've modified As(III) based on Fe(II), and I've attached the modified file for your review (I would appreciate confirmation that I've made these modifications correctly). I've also added the following lines to my PDB file at the potential binding location:
HETATM 1598 AS AS3 X 1 -0.536 -0.448 -8.946 1.00 23.65 AS
I would greatly appreciate any feedback, suggestions, or concerns you may have about this approach. Your expertise would be invaluable in helping me refine my methodology.
Thank you for your time.