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<DIV>Hello,</DIV>
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<DIV>I'm also running SV on a membrane protein in 150 mM NaCl, 50 mM NaCl, and 0.1 % Foscholine-12.</DIV>
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<DIV>I have no data for the detergent density or viscosity and so I tried to omit it completely from the input parameters and see what sedfit c(s) would output. </DIV>
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<DIV>The mass values were way off from what was expected... as expected.</DIV>
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<DIV>Can anyone suggest a way I can deal with density, viscosity, vbar (without actually measuring the density) for this buffer / detergent combination?</DIV>
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<DIV>Cheers</DIV>
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<DIV>Mark</DIV>
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<DIV>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,<BR>Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH <BR>Tel: +44 1382 386095 Fax: +44 1382 345764 Mobile: 07525 451 117<BR>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</DIV>
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<DIV>************************************************************<BR><FONT color=#666666>Please consider the environment. Do you really need to print this email?</FONT> </DIV><BR><BR>>>> Chad Brautigam <chad.brautigam@utsouthwestern.edu> 5/13/2010 15:41 >>><BR>Greetings, All, from the newbiest of membrane-protein newbies,<BR><BR>First, let me thank all of you experts who answered (both on- and off- <BR>board) my last question on the topic of membrane proteins. 'Preciate <BR>ya, as we say here in Texas.<BR><BR>I recently did some SV experiments on a membrane protein solubilized <BR>in the accursed floating detergent LDAO (DDAO to some of you). I was <BR>able to fit the data nicely in SEDFIT using a discrete species model. <BR>By using the trick of setting the vbar to 0, I fitted for s and for <BR>the buoyant molar mass (Mb). Hooray.<BR><BR>In a separate experiment, I used a combination of interference optics <BR>and absorbance optics to measure the amount of detergent bound to the <BR>protein. This was very consistent from sample to sample (I tried 2 <BR>different protein concentrations). This method is à la le Maire et al <BR>(2008) Nat. Protocols, vol. 3, 1782.<BR><BR>OK, so I have Mb and I know the amount of detergent bound to the <BR>protein on a g/g basis (this quantity is deltasubD).<BR><BR>We have the justly famous formula:<BR>Mp = Mb (1-phiprime*rho),<BR>where (neglecting bound lipid)<BR>(1 - phiprime*rho) = (1 - vbarp*rho) + deltasubD(1-vbarD*rho)<BR><BR>So, since I have Mb and deltasubD, and I know rho and the vbars, can I <BR>just plug the Mb that I get from SV into these equations and get a <BR>good estimate for Mp, or is there some SV subtlety here that my newbie <BR>brain hasn't apprehended? I know this can be done for SE, but I've <BR>never seen anyone attempt it for SV.<BR><BR>Any and all responses will be 'preciated.<BR><BR>Chad<BR><BR>======================================<BR>Chad A. Brautigam, Ph.D.<BR>Assistant Professor<BR>Department of Biochemistry<BR>The University of Texas<BR>Southwestern Medical Center at Dallas<BR>Department of Biochemistry<BR>5323 Harry Hines Blvd.<BR>Rm. ND10.214A<BR>Dallas, TX 75390-8816<BR>Office: 214-645-6384<BR>Fax: 214-645-6353<BR>Email: chad.brautigam@utsouthwestern.edu<BR><BR><BR><BR><BR><BR>_______________________________________________<BR>RASMB mailing list<BR>RASMB@rasmb.bbri.org<BR><A href="http://rasmb.bbri.org/cgi-bin/mailman/listinfo/rasmb">http://rasmb.bbri.org/cgi-bin/mailman/listinfo/rasmb</A><BR></DIV><BR>
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