Re: Advice on heteroatoms, metals and water

[Karsten Suhre <>]

Hi!

Thank you for this information. In fact, I was hoping that Modeller had some 
forcefields hidden somewhere in the depth of its code to do loop modelling 
around  Ca2+ binding sites. The real problem is not to place the Ca2+, but to 
have all the oxygens of the different side chains point its way. My templates 
are not close enough to get this right, and I have even one case where the 
Ca-binding site is only present in the target.

In parallel, I try to get the sidechains in place using Amber, but modelling a 
Ca2+ binding site seems not to be a standard procedure (although this should 
occur quite often). Another problem with Amber is that I would have to keep 
the rest of my protein restrained (otherwise my structure would drift away 
from its crystall-structure status by completely resolving it in water - but 
I want to use the model for protein crystal structure building later). So the 
choice of these restrains turns out to be quite tricky as well.

So I am still wondering whether it would not be possible to teach MODELLER how 
to model a Ca2+ in its loop refinement algorithm. If someone could give me 
some technical advice on how to do this (or where to find more specific 
documentation) I would be very grateful.

Kind regards, Karsten.




On Tuesday 19 August 2003 21:04, Jim Procter wrote:
> Hi. This is directed to :
> >Karsten Suhre <>  (IGS)
> >Introduction of a Ca binding site
> >
> >Moshe Amitay <>  ("Bar-Ilan University, Ramat-Gan,
> >building a model with water molecules.
>
> From: Tjaart de Beer <>
>
> >Modelling with metals and hetero.
>
> The practical advice :
> Modeller treats the 'hetatm' entries as residues for much of the modelling
> process. By this, I mean that it is as picky as with the other residue
> entries when you describe them in the alignment. You can see all the types
> of residue entry that it knows about in the mod6v2/lib/restyp.lib file.
>
> Its always simpler to 'SET HETATM_IO', rather than change the pdb file. If
> modeller knows about the heteroatom residue code then it will read it, and
> not attempt to attach proximal metal ions to the polypeptide backbone.
>
> I was mislead by the chain break character '/', which actually introduces a
> chain break for your model, rather than describing a corresponding template
> (? not really sure here). I got away with this example :
> 1tem:Template:1: :3: :.:.:.
> WLMzz*
>
> 1hom:Homolog:1: :3: :.:.:.
> WITzz*
>
> Where I just used set HETATOM_IO on. The important thing is the numbering
> used in the PIR header for each protein sequence - this only relates to the
> amino acids, not the hereroatoms.
>
> I imagine that you need to use set WATER_IO on, and put in the waters, too,
> but the chain break didn't seem to help.
>
> Above all, look carefully at the numbers that Modeller gives you when it
> complains that you don't have enough residues in the PDB file or the
> sequence. For Moshe's case, the chain break may well have been the problem,
> but it can't hurt to use the unedited PDB file but setting HETATM_IO as
> well as WATER_IO (but maybe you could delete the un-necessary waters and
> heteroatoms from the pdb file just to make the alignment simpler!).
>
> As for the optimization behaviour with metal atoms - I didn't really notice
> modeller doing any optimization of the bonding geometry, but in my case
> these contacts were thoroughly conserved. However, I can't see any
> parameters in the MD forcefield definitions to indicate that charge/ligand
> geometry is taken into account, it is probably all done through restraints.
>
> Think thats it - sorry for not giving a concrete example!
>
> j--
>
> ps. For Calcium - the HETATM's residue entry should be CAL or CA (that is,
> not CA2), and '3' is the alignment symbol used in the PIR file (see the
> restyp.lib file).
> _______________________________________________________________________
> Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics
> Hamburg       http://www.zbh.uni-hamburg.de/mitarbeiter/procter

-- 
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