[RASMB] v-bar calculation

[Arthur Rowe]

Hi Chun -

The partial specific volume of a solute component in solution is technically
the partial derivative of the volume of the system (the solution) with
respect to change in concentration (usually expressed in g/ml) of the
component - at given temperature, pressure and solute concentration. More
colloquially, it is described as the increase in volume of the system when 1
g of solute is added to an infinite volume of system.

To a still easier to grasp definition, it is (more or less) the reciprocal
of the density of the solute component. On this basis, it can be computed
(e.g. by SEDNTERP, BIOMOLS or any other appropriate software by summing up
the partial volumes of the constituent amino acids, weighted in accordance
with their occurrence in the protein. This is known as "Traube's Rule".
Amazingly, it works pretty well. The reason is that two effects which would
tend to invalidate Traube's Rule are of opposite algebraic sign, so mostly
cancel out:

(1) the water bound to protein is on average bound at a density higher than
free water, so adding solute adds less volume to the system than you would
predict. Effect: to decrease vbar by around 0.02 ml/g

(2) there are voids within proteins, associated with the non-perfect packing
of constituent amino-acids - so adding protein to a system adds more volume
than you would expect. Effect: to increase vbar by around 0.02 ml/g !

So - computing vbar is an approximation, but a reasonably good one so long
as you stick to 'normal' solvents (e.g. the above arguments are not true in
8M urea etc). As regards post-translational modification of the type you
suggest, any effect is within the error horizon of the method.
Glycolsylation is a different matter, however. You need to know what
percentage of glyco you have, and then do a weighted average vbar, taking
0.63 ml/g as a guesstimate for the glyco bit is probably OK.

All best

Arthur Rowe

--
*******************************************************
Arthur J Rowe
Professor of Biomolecular Technology
NCMH Business Centre
University of Nottingham
School of Biosciences
Sutton Bonington
Leicestershire LE12 5RD   UK

Tel:        +44 (0)115 951 6156
            +44 (0)116 271 4502
Fax:        +44 (0)115 951 6157
email:      arthur.rowe at nottingham.ac.uk
            arthur.rowe at connectfree.co.uk (home)
Web:        www.nottingham.ac.uk/ncmh/business
*******************************************************


From: Chun Tang <tang at hhmi.umbc.edu>
Date: Tue, 15 Jul 2003 19:11:59 -0400
To: rasmb at rasmb-email.bbri.org
Subject: [RASMB] v-bar calculation
Resent-From: Chun Tang <tang at hhmi.umbc.edu>
Resent-To: rasmb at rasmb-email.bbri.org
Resent-Date: Wed, 16 Jul 2003 12:09:03 -0400


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Hi,

I know this question must have been asked many times before. What is exact
meaning of partial specific volume? I can calculate v-bar using program
SEDNTERP. What corrections I need to make when the protein is
post-translationlly modified, e.g myristoylation, phosophorylation. Thanks
in advance for your kind replies.

Best regards,

Chun




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