From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Thu Sep 01 2011 - 04:09:16 CDT
Sorry if not clear enough. First GRID have a option to 'account' amino
acid side chains flexibility, but same program must be 'applied' on
'static' protein structure. As you state that on the basis of
experiments know approximate part of your protein where Zn ion should
bind, you should decide do you want to account for protein flexibility
or not. For sure MD trajectories with bound metal ion will be different
comparing to same protein without metal ion. Generally Zn often have a
affinity to loops that are per se flexible, as well as could be found on
the interfaces, for example between to alpha helix. So I suggest to
first perform MD simulation for protein alone, to see is there
significant movement in region where you expect that Zn bind, than to
estimate affinity of Zn for this region, place an ion, and repeat MD for
the 'metalloprotein'. Hope that can be sueful
On 9/1/2011 4:51 AM, Andrea Holfelder wrote:
> Thanks Mr.Branko
> I did not quite understand your last point though,
> "than try with few snapshots from trajectory which have significantly
> different conformations in the region where Zn ion could bind well"
> Are you suggesting to do a different MD for protein alone and then a
> different MD for metalloprotein and see the significant changes in
> region where Zn could bind well etc. ?
> Care to elaborate,please Mr Branko?
>> ----- Original Message -----
>> From: Branko
>> Sent: 09/01/11 01:58 AM
>> To: Andrea Holfelder, namd-l
>> Subject: Re: namd-l: Dock a metal ion into a peptide/protein
>> This is not a question for NAMD mailing list; anyway try with the
>> GRID (http://www.moldiscovery.com/soft_grid.php), there you have a
>> Zn2+ probe, and you can estimate positions in your protein with high
>> affinity for it. Good way is to perform classical MD simulation of
>> the protein alone, than try with few snapshots from trajectory which
>> have significantly different conformations in the region where Zn ion
>> could bind well. Hope this will help
>> Kind regards
>> On 8/31/2011 9:29 PM, Andrea Holfelder wrote:
>>> Which is the best software to dock a metal ion into a protein .pdb
>>> file and generate a.pdb file of the "metalloprotein" ?
>>> While not exactly, but by some experiments,I know of a possible
>>> binding site in my protein and it has like pico molar affinity
>>> towards Zn+2 .
>>> Is there a good software to achieve this ?
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