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<BODY style="MARGIN: 4px 4px 1px; FONT: 10pt Tahoma" text=#000000 bgColor=#ffffff><PRE class=moz-signature cols="72"><FONT face=Tahoma>Hello RASMB,</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>Sedfit c(s) analysis of a protein I'm working with shows a 30 kDa peak with S = 2.60 and f/f0 of 1.2, that corresponds to monomer.</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>SOMO in Ultrascan using the pdb file for this protein predicts a 30 kDa monomer at 2.42, with f/f0 of 1.19. It's good agreement with the sedimentation velocity results.</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>However, the crystal structure, SEC, etc. indicate this protein should be a <EM>dimer</EM>.</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>Starting with the default value of 1.2 for the frictional ratio and floating in sedfit returns a value of 1.2, with MW that corresponds to monomer. RMSD = 0.009756</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>Doubling this value to 2.4 and floating gives a value of 2.3, and assigns a mass that corresponds to dimer to the main peak in the c(s) analysis. RMSD = 0.009324</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>Thus there appear to be two energy minima for the frictional ratio, depending which initial value is used. The RMSD value is lower when the higher value of f/f0 is used.</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>Would you, on the basis of RMSD values, assign monomer or dimer to this peak?</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>Thanks,</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>Mark</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma></FONT> </PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<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>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</FONT></PRE><PRE class=moz-signature cols="72"><FONT face=Tahoma></FONT> </PRE>
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