[Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues

[Elaine Meng]

Dear Ingmar,
It sounds like you want to model your whole protein including the 4Fe4S cluster, am I right?  Or is there a structure of your protein but that does not include the cluster?

I would not recommend modeling this "from scratch" (building one atom by one atom) in Chimera but instead, homology-modeling your protein and cluster from the structure of a related protein that contains the cluster.  Of course, this all depends on the existence of a known structure for a related protein. 

Chimera includes an interface to the Modeller program for homology-modeling.   To use it, you would have to first go to the Modeller website 
<http://www.salilab.org/modeller/registration.html>
and register to get a license key (free for academic use).  In Chimera, you could choose "Tools... Sequence... Blast Protein," paste in the sequence of your protein, and then blast it against the PDB to see if there are any structures related to your protein.  If there is a hit that seems good enough to you, you could use the Blast results dialog to open the structure and also the alignment of the two sequences.  
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/blast.html>
Then, in the sequence alignment window, choose "Structure... Modeller Tools" to show the interface to Modeller.  Use "Advanced Option" to "Include non-water HETATM residues from template" so that the FeS cluster will be included in the model.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>

Or, you could simply see if there is already a model of your protein available in ModBase by using "File... Fetch by ID" in the Chimera menu.  However, those models probably wouldn't contain the FeS cluster.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html>

Some related references I just saw but didn't read in detail:

Fee, J. A.; Castagnetto, J.M.; Case, David A.; Noodleman, L.; Stout, C.D.; Torres, R.A.; "The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526. 
<http://dx.doi.org/10.1007/s00775-003-0445-8>

Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. 
(2002) J.Mol.Biol. 315: 1155-1166
<http://dx.doi.org/10.1006/jmbi.2001.5292>
(goes with PDB entries 1iqz, 1ir0 ... I see that the residue name of the cluster is SF4, so you could also use the searching tools at the PDB website to find structures that have this cluster)

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 6, 2011, at 6:44 AM, Ingmar Buerstel wrote:
> Dear users,
> i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self.  I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. 
>  
> So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster 
> Thanx in advance,  
> Ingmar