[RASMB] vbar of protein binding zinc and copper ions

HGSR (Holger Martin Strauss) hgsr at novonordisk.com
Fri Feb 28 00:56:16 PST 2014


Bonjour Christine,

Just a thought, a little besides the indeed interesting question, what "really" is happening. Not knowing your exact question and the system under study, I would venture that for most cases it could be sufficient to define your solute as the metal-free entity and the metal as a solvent component. This way, you will still be able to study metal-dependent oligomerisation changes with changes in [metal ion]. For studying metal ion binding to peptides without changes in the oligomerisation per se, you might still get enough precision for (1-vbar rho)M from an SE-gradient to back-calculate the change in vbar. Coupled changes in shape/hydra-solvation-whatever you could get by combining this with measurements of the diffusion coefficient, which is independent of the solute density. Thermodynamic information for the metal binding you could get from other, mass-independent methods.

But still, for further reference, it would be nice to have someone bite the bullet ( and working with insulins, I'm not pointing fingers here).

Cheers, Holger

From: rasmb-bounces at list.rasmb.org [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of Mattia Rocco
Sent: Thursday, February 27, 2014 6:46 PM
To: Laue, Thomas; EBEL Christine; rasmb at list.rasmb.org
Subject: Re: [RASMB] vbar of protein binding zinc and copper ions


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<mailto: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<mailto: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


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