[RASMB] sedfit vs SOMO vs structure

Mark Agacan M.Agacan at dundee.ac.uk
Fri Jul 8 03:08:47 PDT 2011


Hello RASMB,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.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.However, the crystal structure, SEC, etc. indicate this protein should be a dimer.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 = 0.009756Doubling 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 = 0.009324Thus 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.Would you, on the basis of RMSD values, assign monomer or dimer to this peak?Thanks,Mark ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery,
Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH 
Tel: +44 1382 386095    Fax: +44 1382 345764    Mobile: 07525 451 117
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