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<div>Hi Marina,</div><div> </div><div> A couple of points: </div><div><br class="webkit-block-placeholder"></div><div>First, gel filtration cannot give you a molar mass. It can give you only a Stokes radius.</div><div><br class="webkit-block-placeholder"></div><div>Second SEDFIT does not have a monomer-hexamer model that can be used for direct fitting to a monomer-hexamer model.</div><div><br class="webkit-block-placeholder"></div><div>If the material is pure and exhibits no concentration dependence you can use SEDFIT c(s) and C(M) to get the molecular weight.</div><div><br class="webkit-block-placeholder"></div><div>However if it is reversibly associating/dissociating, you will need to use other software, like SEDANAL, in which you can specify a model of your choice.</div><div><br class="webkit-block-placeholder"></div><div>Of course, you can use SEDANAL also to get the molar mass of non-interacting species as well without making any assumptions about frictional ratios.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>Walter F. Stafford</div><div>Senior Scientist</div><div>Boston Biomedical Research Institute</div><div>64 Grove Street</div><div>Watertown, MA 02472</div><div>617-658-7808</div><div><a href="mailto:stafford@bbri.org">stafford@bbri.org</a></div><div><br class="webkit-block-placeholder"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></span></span> </div><br><div><div>On Mar 3, 2008, at 04:10, Fasolini, Marina [Nervianoms] wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div><span class="726354713-28022008"><span class="591374208-03032008"><font face="Arial" size="2">Dear AUC users,</font></span></span></div> <div><span class="726354713-28022008"><font face="Arial" size="2"><span class="591374208-03032008">I have a problem in the fitting of some data and I would like to have your opinion.</span></font></span></div> <div><span class="726354713-28022008"><font face="Arial" size="2"><span class="591374208-03032008"></span></font></span> </div> <div><span class="726354713-28022008"><font face="Arial"><font size="2">I want to control the sedimentation of<span class="591374208-03032008"> </span><span class="591374208-03032008">a </span>protein in order to define the state of oligomerization. <span class="591374208-03032008">It is published as forming an <span class="591374208-03032008"> h</span>e<span class="591374208-03032008">x</span>americ homo oligomer.<span class="591374208-03032008"> </span>From the crystal structure, i</span>t is a wheel like structure of 160<span class="591374208-03032008"> angstrom</span><span class="591374208-03032008"> </span> in diameter, with a central role of 15<span class="591374208-03032008"> </span>angstrom in diameter.<span class="591374208-03032008"> </span><span class="591374208-03032008">The thickness is 20-40 angstrom. How can I expect it to sediment? How can I improve my parameters or model in order to improve the fitting?</span></font></font></span></div> <div><span class="726354713-28022008"><font face="Arial" size="2"><span class="591374208-03032008"></span></font></span> </div> <div><span class="726354713-28022008"><font face="Arial" size="2">The protein is 50KDa <span class="591374208-03032008"> but in </span>gel filtration it cames out as <span class="591374208-03032008"> hexamer (300 KDa)</span>.<span class="591374208-03032008"> </span>In my sedimentation experiment I see <span class="591374208-03032008">one </span>peak of <span class="591374208-03032008"> 6.23S which corresponds to </span>140KDa. <span class="591374208-03032008"><font color="#0000ff">Fitting of the sedimentation data was done with SedFit. </font></span><span class="591374208-03032008">D</span>o you think I can say that it is a trimer? I would expect it as an <span class="591374208-03032008">h</span>examer.</font></span></div> <div><span class="726354713-28022008"><font face="Arial" size="2"></font></span> </div> <div><span class="726354713-28022008"><font face="Arial"><font size="2">I hope someo<font color="#0000ff"><span class="591374208-03032008">ne</span><span class="591374208-03032008"> can</span></font> help me<span class="591374208-03032008"><font color="#0000ff">. </font></span></font></font></span></div> <div><span class="726354713-28022008"><font face="Arial"><font color="#0000ff" size="2"><span class="591374208-03032008"></span></font></font></span> </div> <div><span class="726354713-28022008"><font face="Arial" size="2">the conditions are :</font></span><span class="726354713-28022008"><font face="Arial" size="2"> </font></span></div> <div> <div class="O" v:shape="_x0000_s2050"> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><font face="Arial" size="2">buffer 20mM Tris pH7, 150mM NaCl, 1mM DTT, 5%gly </font></span></div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><font face="Arial" size="2">Vbar 0.7397 </font></span></div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><font face="Arial" size="2">Viscosity 1.02530 </font></span></div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><font face="Arial" size="2">Density 0.01183 </font></span></div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><font face="Arial" size="2"></font></span> </div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><span class="726354713-28022008"><font face="Arial" size="2">Thanks a lot</font></span></span></div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><span class="726354713-28022008"><font face="Arial"><font size="2">Marina<span class="591374208-03032008"> </span></font></font></span></span></div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><span class="726354713-28022008"><font size="2"><span class="591374208-03032008"></span></font></span></span> </div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><span class="726354713-28022008"><font size="2"><span class="591374208-03032008"></span></font></span></span> </div> <div style="mso-line-spacing: '100 50 0'; mso-char-wrap: 1; mso-kinsoku-overflow: 1"><span style="FONT-SIZE: 58%"><span class="726354713-28022008"><font size="2"><span class="591374208-03032008"> </span></font></span></span></div> <div style="mso-line-spacing: '100 50 0'"><span style="mso-special-format: lastCR"><font face="Arial" size="2"></font></span></div></div></div> <div><font face="Arial" size="2">MARINA FASOLINI</font></div> <div><font face="Arial" size="2">Structural Chemistry </font></div> <div><font face="Arial" size="2"><a href="http://www.nervianoms.com/">Nerviano Medical Sciences</a></font></div> <div><font face="Arial" size="2">Viale Pasteur 10</font></div> <div><font face="Arial" size="2">20014 Nerviano - </font><font face="Arial" size="2">Milano</font></div> <div><font face="Arial" size="2"><a href="mailto:marina.fasolini@nervianoms.com">marina.fasolini@nervianoms.com</a></font></div> <div><font face="Arial" size="2">Tel. +390331581462</font></div> <div><font face="Arial" size="2">Fax. +390331581360</font></div> <div> </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">RASMB mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:RASMB@rasmb.bbri.org">RASMB@rasmb.bbri.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://rasmb.bbri.org/mailman/listinfo/rasmb">http://rasmb.bbri.org/mailman/listinfo/rasmb</a></div> </blockquote></div><br></body></html>