[gmx-users] Binding Copper to Protein

[Tsjerk Wassenaar]

Hi,

Justin raises a number of problems, but there's another one. Copper is
a transition metal with a specific coordination which depends on the
oxidation state. If you only use bonds, you sort of assume that the
coordination geometry is the result of a size-exclusion effect. In
this respect, copper is to be regarded an exotic species:

http://wiki.gromacs.org/index.php/Exotic_Species

Cheers,

Tsjerk

On Sat, Mar 21, 2009 at 1:05 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> DimitryASuplatov wrote:
>>
>> Hello,
>> I am working with enzyme that contains Cu2+ in the active site. During a
>> free simulation it always gets out due to minor conformational changes
>> of coordinating residues. Since the copper is known to be essential for
>> enzyme catalysis I want to set some extra force to bind it to certain
>> residues.
>>
>> 1/ I have not found CU2+ in opls ff. In ions.itp CU is defined as CU2+
>> atomtype which I think is taken from GMX ff. Is it correct to use GMX
>> Copper parametrization with OPLS?
>>
>
> If you are ever asking yourself, "Can I take part of one force field and
> introduce it into another?" the answer is always *absolutely not.*
>
> However, CU2+ is part of OPLS (in ions.itp, there is CU2+ after #ifdef
> _FF_OPLS), and a reference for these parameters is given in ffoplsaa.atp.
>
>> 2/ What is the easiest way to bind a metal ion to a histidine residue?
>> What if I add the bond to specbonds.dat without changing HIS topology
>> (dihedral can be set to 0 0 0 0 0 0 in the itp file of the protein)? Can
>> this be correct?
>>
>
> You can try it and see.  Whether or not you think it's appropriate is going
> to depend on what is known about your particular system.  But if you are
> defining a bonded interaction of any sort between a metal ion and an amino
> acid side chain, I would argue that the original HIS topology is no longer
> valid, since it is sharing electrons with the metal, thus affecting the
> charge of all species involved in the bonded interaction.
>
> -Justin
>
>> Thanks. I appreciate your time.
>> SDA
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623