Hello Prof. Case,
I am aware that you are an expert on iron sulfur complexes found in proteins and have located one of your classic papers on the issue (Noddleman & Case, Adv. Inorg. Chem. 38:423-458 (1992)) but our library does not have a copy of this series (hard to believe, I know). Do you by any chance have a reprint you could share?
I have been studying Xanthine oxidase (1FIQ), a protein that contains an Fe2S2 group, one of the smaller of such clusters. I am quite well aware of the need to revise the parameters for the CYS residues that connect this cluster to the protein, but it is not clear to me how to do this. If I carry out an Oniom calculation in g09, I can include these CYS residues and eventually perhaps get ESP charges for the whole set of atoms that include the cluster and the CYS residues. However such a procedure does not guarantee that the partial charges are consistent with those assigned to the rest of the protein. I am hoping that by reading your paper I can have a handle on the charge state to assign to this smaller iron-sulfur cluster, as that is not clear to me either. I have no experience in the full development of force field parameters yet - it seems that this problem requires me to learn about that.
If you have any material that is relevant to this iron-sulfur complex that you could share, or specific suggestions, I would be much appreciative.
Thanks,
Sergio Aragon
Professor of Chemistry
San Francisco State University
-----Original Message-----
From: case [mailto:case.biomaps.rutgers.edu]
Sent: Wednesday, June 05, 2013 12:41 PM
To: AMBER Mailing List
Subject: Re: [AMBER] iron-sulfur parameterization
On Thu, Jun 06, 2013, venkatesh s wrote:
>
> i am struggling with iron-sulfur cluster parametrization
> Unknown residue: SF4 number: 0 type: Terminal/last
This is a difficult problem: iron sulfur cubane clusters come in three oxidation states, and reliable vibrational spectra have only recently become available. One not only needs parameters for FS4, but also revised parameters for the four CYS residues that are connects to the iron-sulfur cubane.
We are working to prepare a set of files that will allow such active sites to be modeled, but this is still a work in progress, and more testing is needed.
Some CHARMM force field parameters for the 2- state are discussed by Mitra et al. Biochemistry 50:5220, 2011. These may help, but you will need to know a lot about force fields and how they are represented in Amber parameter files. It's not just a matter of loading a PDB file.
...regards...dac
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Received on Wed Jun 05 2013 - 13:30:03 PDT
