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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman">Happy New Year to you all<SPAN
class=663571020-03012005>.</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">If
you are interested in doing <SPAN class=663571020-03012005>protein</SPAN>
self-association modeling exercise, this is for you.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman"></FONT> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">The
XLA raw data set <SPAN class=663571020-03012005>are</SPAN> provided here.
The rule is simple. You can use <SPAN class=663571020-03012005>any of
</SPAN>your favorite software to come up with a plausible model. The goal is to
see if <SPAN class=663571020-03012005>people </SPAN>performing this
exercise<SPAN class=663571020-03012005>, using one's
favorite software,</SPAN> will <SPAN
class=663571020-03012005>the</SPAN> the same model<SPAN
class=663571020-03012005> </SPAN><SPAN class=663571020-03012005>(picture)
</SPAN><SPAN class=663571020-03012005>emerge?</SPAN><SPAN
class=663571020-03012005> If </SPAN>not, why not?</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">Last
Christmas I encountered this interesting protein. The protein sequence is
known<SPAN class=663571020-03012005>. </SPAN><SPAN class=663571020-03012005>It
</SPAN>is about 91<SPAN class=663571020-03012005> </SPAN><SPAN
class=663571020-03012005>KD</SPAN> for the monomer. Also the EM <SPAN
class=663571020-03012005>picture </SPAN>is available<SPAN
class=663571020-03012005>.</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
class=663571020-03012005></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">The
protein is in 25 mM HEPES, 0.1mM EGTA, 200mM KCl.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">I
ran SV (30K speed) and SE (7K and 8.5K speed) experiment at 4C. Fresh samples
were used for each experiment.<o:p></o:p></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">For
analysis I used v-bar=0.7167, rho=1.0084, viscosity=1.0064E-2 (all values are
obtained from SEDNTERP but contributions from HEPES and EGTA were
omitted)</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">To
get the apparent MW, I used scan 7 from the SE experiment and selected subset
radius ranges from ~6.9cm to 7.12cm.<SPAN style="mso-spacerun: yes">
</SPAN>I then subsequently used the same radius range for self-association model
fitting to make the modeling comparisons more meaningful and more consistent.
</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">For
SV data analysis, I used SEDFIT and used all 186 scans for analysis. I also used
SEDNTERP to convert S4c,w to S20c,w. </FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="mso-spacerun: yes"><FONT face="Times New Roman"> </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">For
SE data analysis I used SEGAL and SEDPHAT and also Origin to get a
ballpark <SPAN class=663571020-03012005>value</SPAN> for the apparent
molecular weight.<SPAN style="mso-spacerun: yes"> </SPAN>I took a look at
scan 7 (20 hours) and also scan 10 (26 hours) for the 7K speed. I also took a
look at scan 15 at 8.5K speed.<SPAN style="mso-spacerun: yes">
</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">For
model fitting I chose scan 7 from the SE experiment and selected subset radius
range from ~6.9cm to 7.12cm.<SPAN style="mso-spacerun: yes"> </SPAN>I used
Beckman’s <SPAN class=663571020-03012005>O</SPAN>riginal software to
perform modeling analysis and used variance (goodness of fit) as a guide to
reach my conclusion.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">I
posted my data analysis and fitting results after the raw <SPAN
class=663571020-03012005>compressed </SPAN>data <SPAN
class=663571020-03012005>set, </SPAN>in case you are interested in comparing the
model that I came up with using Beckman Origin 4.1 software.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">Have
fun!</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face="Times New Roman">With
warm regards,</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><o:p><FONT
face="Times New Roman"> </FONT></o:p></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT
face="Times New Roman">Chris</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"></FONT></P></DIV>
<DIV class=Section1 align=left>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px" align=left><FONT
size=3><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px" align=left><FONT
size=3><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px" align=left><FONT
size=3><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px" align=left><FONT
size=3><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px" align=left><FONT
size=3><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">-------------------------------------------------------------</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><SPAN
style="FONT-SIZE: 12pt"><FONT face=Arial>Christopher Chin</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><SPAN
style="FONT-SIZE: 12pt"><FONT face=Arial>Manager</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><SPAN
style="FONT-SIZE: 12pt"><FONT face=Arial>Sealy Center for Structural
Biology</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><SPAN
style="FONT-SIZE: 12pt"><FONT face=Arial>HBC&G, 5134 MRB.
rt1055</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><SPAN
style="FONT-SIZE: 12pt"><FONT face=Arial>UTMB </FONT><A
href="mailto:cchin@utmb.edu"><FONT face=Arial>cchin@utmb.edu</FONT></A><FONT
face=Arial>, </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><SPAN
style="FONT-SIZE: 12pt"><FONT face=Arial>409-772-1693, efax
630-604-3416</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px"><SPAN
style="FONT-SIZE: 12pt"></SPAN><SPAN style="FONT-SIZE: 12pt"><FONT
face=Arial>-------------------------------------------------</FONT></SPAN></P></DIV>
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