Re: ions behavior in protein-water box:

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Wed Oct 29 2008 - 17:12:23 CDT

Ema,

I agree that the ions shouldn't effect the protein dramatically, but
if you are concerned with the interactions of the ions with the
protein why include the Ca2+ and not just Na+? If the protein is not
restrained in any way the ion effect over the length of the simulation
should not be too dramatic. Simple Brownian motion is going to move
the ions with or without the protein.

Best,
Chris

On Oct 29, 2008, at 5:56 PM, Emanuelle Bachelet wrote:

> Hi Chris,
>
> By closer I mean less than 5A, I haven't measured the exact distance
> because it's fluctuating. But imo, less than 5A means ions are going
> to modify the electrostatic interactions with/on the protein. Ions
> should be just to neutralize the system not to interact with the
> protein.
>
> I will also have a look at the reference you mention.
>
> Thanks,
> Ema
>
> On Wed, Oct 29, 2008 at 4:05 PM, Christopher Gillespie <gillescche_at_gmail.com
> > wrote:
> Ema,
>
> What exactly do you mean by "closer"? Ion association with protein
> surfaces is not necessarily an "incorrect" observation rather ions
> can interact with various parts routinely. Take a look at the work
> of Pavel Jungwirth on ion protein association.
>
> Best
>
> Chris
>
>
>
> On Oct 29, 2008, at 2:44 PM, Emanuelle Bachelet wrote:
>
> Hello,
>
> I have a question regarding ions in a simulation.
>
> I have a protein that has a net charge of -9 (it includes one of the
> residues which is phosphorylated). I immersed this protein in water
> box it and added 4 calcium ions and one sodium ion to neutralize the
> overall charge.
>
> But when my simulation system reaches .5ns of production dynamics
> (NVE), some ions move closer to the protein. In my opinion, they
> should not come too close to protein so as to modify the protein
> behavior. Does this mean that I constrain the ions at a particular
> position?
>
> thanks,
> Ema.
>
>

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