> On Mar 17, 2022, at 3:00 AM, amber-request.ambermd.org wrote:
>
> Subject: Re: [AMBER] question about ATP-Mg2+ binding system
> Message-ID:
> <20220316173510.einhofh7uhznzcpv.rbsbrr1029l01.rad.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Wed, Mar 16, 2022, liu kai wrote:
>
>> After few ns production run, I found two Na+ ions close (about 2.5 Angstrom)
>> to the phosphate group, except the Mg2+.
>
> Can be elaborate here? Do you mean that the Mg2+ left the vicinity of the
> ATP? Or do you mean that the Na+ ions came close to the phosphate oxygens,
> but not close to the Mg2+?
>
>> I think the Na+ should not be close to the phosphate group.
>> If the simulation is correct, does it mean that ATP can coordinate with
>> two Mg2+ ions at the same time?
>
> A single Mg2+ only neutralizes part of the -4 charge of ATP. So other
> cations are certain to come close during MD. Why to you think that Na+ ions
> should not come close? The origin of your question about two Mg2+ ions is
> not clear to me: did you see this sort of behavior in your simulation?
>
> The Buelens et al. paper you cite is a good starting point here. Carlos'
> questions about what ion and water models you are using are also good
> points. Commenting on the relative concentrations of monovalent and
> divalent ions would also help.
>
> ....good luck….
Currently, I use amber20 for the simulaiton.
The force field ff14SB, TIP3P and 12-6 force field for protein, water and Na+/Mg2+, respectively.
At the beginning of simulation, ATP4- and Mg2+ in the pocket of protein as that of PDB file, while
6 Na+ counter ions surround the protein, far away from ATP-Mg binding pocket.
During the simulation, the relative distance between ATP-Mg was maintained.
In addition, two Na+ ions was close to ATP.
I understand that "A single Mg2+ only neutralizes part of the -4 charge of ATP. So other
cations are certain to come close during MD. “
My questions are:
1. Assuming if only Mg2+ ions in the simulation, there should be two Mg2+ around ATP (-4).
But why only one Mg2+ was found in the PDB file?
2. Would the water surrounding ATP hinder the cation ion approach?
3. Is the charge of phosphate group of ATP too negative?
.Carlos I will read the document of 12-6-4 charge and try it.
Yours sincerely,
Kai
> dac
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Received on Wed Mar 16 2022 - 19:30:02 PDT
