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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear John,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Good afternoon – there are two
references I use regularly for the calculation of partial specific volumes for small
molecule species. These are:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Durchschlag, H. & Zipper, P.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Calculation of the partial specific volume
of organic compounds and polymers<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Progress in Colloid and Polymer Science,
94, 20 – 39 (1994)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Durchschlag, H. & Zipper, P.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Calculation of the partial specific volumes
and other volumetric properties of small molecules and polymers<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Journal of Applied Crystallography, 30,
803 – 807 (1997)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>The supplementary material for this
article is extremely helpful.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hope this is of help.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Kind regards, Rodolfo<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
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<p class=MsoNormal><font size=2 color=navy face="Times New Roman"><span
style='font-size:10.0pt;color:navy'>Rodolfo Ghirlando Ph.D.</span></font><font
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<p class=MsoNormal><font size=2 color=navy face="Times New Roman"><span
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<p class=MsoNormal><font size=2 color=navy face="Times New Roman"><span
style='font-size:10.0pt;color:navy'>Laboratory of Molecular Biology</span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face="Times New Roman"><span
style='font-size:10.0pt;color:navy'>NIDDK-NIH-DHHS</span></font><font
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style='font-size:12.0pt;color:navy'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face="Times New Roman"><span
style='font-size:10.0pt;color:navy'>Tel: 301-451-8158</span></font><font
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<p class=MsoNormal><font size=2 color=navy face="Times New Roman"><span
style='font-size:10.0pt;color:navy'>E-mail: <a
href="mailto:rodolfo.ghirlando@nih.gov">rodolfo.ghirlando@nih.gov</a></span></font><font
color=navy><span style='color:navy'><o:p></o:p></span></font></p>
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<p class=MsoNormal><b><font size=1 color="#76923c" face=Candara><span
style='font-size:9.0pt;font-family:Candara;color:#76923C;font-weight:bold'>www.niddk.nih.gov<o:p></o:p></span></font></b></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
john_doran@vrtx.com [mailto:john_doran@vrtx.com] <br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, October 17, 2012
5:22 PM<br>
<b><span style='font-weight:bold'>To:</span></b> rasmb@rasmb.bbri.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [RASMB] Is there a facile
method to get Vbar for small molecules without using densitometry?</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=sans-serif><span style='font-size:10.0pt;
font-family:sans-serif'>Greetings fellow Rasmb members</span></font><br>
<br>
<font size=2 face=sans-serif><span style='font-size:10.0pt;font-family:sans-serif'>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? </span></font><br>
<br>
<font size=2 face=sans-serif><span style='font-size:10.0pt;font-family:sans-serif'>Thank
you in advance for any replies that are sent to address this problem!</span></font><br>
<br>
<br>
<font size=2 face=sans-serif><span style='font-size:10.0pt;font-family:sans-serif'>John
D Doran, Ph.D.<br>
Protein Biochemistry<br>
Vertex Pharmaceuticals Inc.<br>
130 Waverly Street<br>
<st1:place w:st="on"><st1:City w:st="on">Cambridge</st1:City>, <st1:State
w:st="on">MA</st1:State> <st1:PostalCode w:st="on">02139</st1:PostalCode></st1:place><br>
617-444-6142</span></font><o:p></o:p></p>
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