[RASMB] Is there a facile method to get Vbar for small molecules without using densitometry?

[Ghirlando, Rodolfo (NIH/NIDDK) [E]]

Dear John,

Good afternoon - there are two references I use regularly for the calculation of partial specific volumes for small molecule species. These are:

Durchschlag, H. & Zipper, P.
Calculation of the partial specific volume of organic compounds and polymers
Progress in Colloid and Polymer Science, 94, 20 - 39 (1994)

Durchschlag, H. & Zipper, P.
Calculation of the partial specific volumes and other volumetric properties of small molecules and polymers
Journal of Applied Crystallography, 30, 803 - 807 (1997)
The supplementary material for this article is extremely helpful.

I have found the calculations described to work reasonably well. In the particular case of a self-associating PNA, the partial specific volume was well determined as the sedimentation equilibrium monomer-dimer Kd using this value correlated with a non v-bar dependent measure using sedimentation velocity.

Hope this is of help.

Kind regards, Rodolfo

________________________________
Rodolfo Ghirlando Ph.D.
Staff Scientist
Laboratory of Molecular Biology
NIDDK-NIH-DHHS
Building 5, Room 208
5 Center Drive MSC 0540
Bethesda MD 20892-0540
USA

Tel: 301-451-8158
Fax: 301-496-0201
E-mail: rodolfo.ghirlando at nih.gov<mailto:rodolfo.ghirlando at nih.gov>

www.niddk.nih.gov
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NIH . . . Turning Discovery Into Health


________________________________
From: john_doran at vrtx.com [mailto:john_doran at vrtx.com]
Sent: Wednesday, October 17, 2012 5:22 PM
To: rasmb at rasmb.bbri.org
Subject: [RASMB] Is there a facile method to get Vbar for small molecules without using densitometry?

Greetings fellow Rasmb members

The issue has arisen on more than one occasion for us to look at the association state of small molecules ( i.e molecules under 1000 MW) using the AUC. When there is plenty of material it is easy enough to directly measure Vbar using densitometry, but of course there are also occasions where the material is precious and there is not nearly enough for densitometry. Does anyone know of any alternative physical methods or getting Vbar values generated from theory that may be used in lieu of densitometry?

Thank you in advance for any replies that are sent to address this problem!


John D Doran, Ph.D.
Protein Biochemistry
Vertex Pharmaceuticals Inc.
130 Waverly Street
Cambridge, MA 02139
617-444-6142
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