Re: Copper ion moving out of the protein towards bulk solvent

From: poker_at_physics.usyd.edu.au
Date: Wed Feb 08 2012 - 18:24:50 CST

You haven't given us enough relevant information to answer definitively.

Think carefully about the system that you constructed. For example,
did you accidentally protonate a histidine that the ion is
coordinating, which results in a steric clash? Besides, you would
ideally want to introduce additional interactions that mimic
ion-complexation at these enzymatic sites. The lack of such electron
interactions is an open issue for classical MD - so an ultimate answer
may lie in QM/MM.

Best of luck.
- P.

Quoting SUBHA KALYAANAMOORTHY <skalyaanamoorth_at_students.latrobe.edu.au>:

> Hi there ,
>
> I am currently working on the zinc-copper metalized superoxide
> dismutase enzyme . The copper ion moves out of the protein towards
> the bulk solvent during the equilibration(NPT) stage. I am unable to
> predict the reason for the same. Any suggestions on this would be
> greatly appreciated.
>
> Thanks
>
> Subha
>

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