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<TITLE>Re: [RASMB] v-bar calculation</TITLE>
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Hi Chun -<BR>
<BR>
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. <BR>
<BR>
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:<BR>
<BR>
(1) the water bound to protein is on average bound at a density <I>higher</I> than free water, so adding solute adds <I>less</I> volume to the system than you would predict. Effect: to <I>decrease</I> vbar by around 0.02 ml/g<BR>
<BR>
(2) there are voids within proteins, associated with the non-perfect packing of constituent amino-acids - so adding protein to a system adds <I>more</I> volume than you would expect. Effect: to <I>increase</I> vbar by around 0.02 ml/g !<BR>
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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.<BR>
<BR>
All best<BR>
<BR>
Arthur Rowe<BR>
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<BLOCKQUOTE><B>From: </B>Chun Tang <tang@hhmi.umbc.edu><BR>
<B>Date: </B>Tue, 15 Jul 2003 19:11:59 -0400<BR>
<B>To: </B>rasmb@rasmb-email.bbri.org<BR>
<B>Subject: </B>[RASMB] v-bar calculation<BR>
<B>Resent-From: </B>Chun Tang <tang@hhmi.umbc.edu><BR>
<B>Resent-To: </B>rasmb@rasmb-email.bbri.org<BR>
<B>Resent-Date: </B>Wed, 16 Jul 2003 12:09:03 -0400<BR>
<BR>
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Hi,<BR>
<BR>
I know this question must have been asked many times before. What is exact<BR>
meaning of partial specific volume? I can calculate v-bar using program<BR>
SEDNTERP. What corrections I need to make when the protein is<BR>
post-translationlly modified, e.g myristoylation, phosophorylation. Thanks<BR>
in advance for your kind replies.<BR>
<BR>
Best regards,<BR>
<BR>
Chun<BR>
<BR>
<BR>
<BR>
<BR>
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