[RASMB] vbar of protein binding zinc and copper ions

Mattia Rocco mattia.rocco at hsanmartino.it
Thu Feb 27 09:46:28 PST 2014


Hi Christine,

I second what Tom and Borries said. Attached you'll find a key paper by H. 
Durchschlag and P. Zipper describing how to compute the vbar of 
macromolecules. They have a table with the molar volumes of ions included. 
If you happen to have a PDB structure for your protein including the ions, 
US-SOMO will compute the global psv, but the caveats pointed out by Tom and 
Borries will still apply...

Salut - Mattia

At 02:02 PM 2/27/2014 +0000, Laue, Thomas wrote:
>Content-Language: en-US
>Content-Type: multipart/alternative;
> 
>boundary="_000_910F1E6B4D39C34FB33F47E069C64D6365CCA349akersadunhedu_"
>
>Hi Christine-
>In general, their contribution will be roughly proportional to the inverse 
>of the metal density in the computation of vbar from composition. The 
>confounding part is that their ionization will cause electrostriction of 
>water, if they remain charged when bound. If the ions are bound in such a 
>way to be neutral (i.e. they are chelated by charged residues), then the 
>approximation using their density will not be as much in error as it would 
>be if they remain charged.
>Best wishes,
>Tom
>
>----------
>From: rasmb-bounces at list.rasmb.org [rasmb-bounces at list.rasmb.org] on 
>behalf of EBEL Christine [christine.ebel at ibs.fr]
>Sent: Thursday, February 27, 2014 4:45 AM
>To: rasmb at list.rasmb.org
>Subject: [RASMB] vbar of protein binding zinc and cupper ions
>
>
>
>Dear all,
>
>
>
>
>
>Does somebody know how bound Zn++ or Cu++ ions affect vbar of proteins?
>
>
>
>
>
>Thank you in advance
>
>
>
>
>Christine
>
>
>
>--
>Institut de Biologie Structurale
>UMR 5075 CEA - CNRS - Univ. Grenoble Alpes
>EPN Campus, 6 rue Jules Horowitz, F-38000 Grenoble
>Tel.: +33 (0)4 5742 8570; Fax: +33 (0)4 7650 1890
>E mail: <mailto:Christine.Ebel at ibs.fr>Christine.Ebel at ibs.fr  http://www.ibs.fr
>_______________________________________________
>RASMB mailing list
>RASMB at list.rasmb.org
>http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org


ATTENZIONE.
Il presente messaggio ed i suoi allegati devono intendersi ad uso esclusivo 
dei suoi destinatari e sono confidenziali. Persone diverse dal 
destinatario, anche ai sensi del D.Lgs. n. 196/2003 , non debbono prendere 
visione dei contenuti, copiare od inoltrare l'e-mail a terzi. Se ricevete 
questo messaggio per errore, Vi preghiamo di cancellarlo, di distruggerne 
ogni copia e di informarci immediatamente. La mail non è un protocollo 
sicuro, pertanto IST declina ogni responsabilità in caso di intercettazione 
o modifiche del presente messaggio.
WARNING.
This message and any attachments is intended solely for the use of the intended
addressees and is confidential. Any unauthorized review, use, disclosure or 
distribution
is prohibited. If you receive this message in error, please delete it, 
destroy all copies
and immediately notify us. Mail is not a secure protocol, therefore IST 
will not be liable
for interception or amendment of this message.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://list.rasmb.org/pipermail/rasmb-rasmb.org/attachments/20140227/98df9166/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ProgCollPolymSciDurchschlag94.pdf
Type: application/octet-stream
Size: 1295926 bytes
Desc: not available
URL: <http://list.rasmb.org/pipermail/rasmb-rasmb.org/attachments/20140227/98df9166/attachment.obj>


More information about the RASMB mailing list