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<TITLE>Re: [RASMB] frctional ratio</TITLE>
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<BLOCKQUOTE><FONT COLOR="#800000">Dear Ewa<BR>
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A spherical, unhydrated protein of mass 41.7 kD would have an expected Rh = 2.3 nm (if a vbar = 0.73 ml/g is assumed). That means a frictional ratio = 4.2/2.3 = <U>1.83</U>. <BR>
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As you have correctly inferred, that is clearly not a simple globular protein, for which a frictional ratio in the region of 1.1-1.2 is expected. There are two possibilities:<BR>
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(1) you have one of these 'natively unfolded' proteins, whose normal state is a loosely structured swollen one, <I>or<BR>
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(2) you have an elongated protein, ball-park axial ratio of around 10 giving a Perrin function (that part of the frictional ratio which can be attributed to shape rather than hydration/swelling) = around 1.5 (derived from 1.83/1.2)<BR>
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If you have done static light LS, you ought to be able to extract an Rg value (you can download a pdf about Rg values etc from rabbit.cbe.uiowa.edu/Regression.pdf) from the slope of the Zimm plot. Unfortunately, the difference between the two models is not great, and SLS does not tend to give values of the precision you can get with SANS or SAXS. <BR>
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If - and its a big IF - you have enough material and the kit to hand to do an intrinsic viscosity <I>and</I> an s upon c plot, you are home and dry, as the Ratio Function ks/[eta] has a value of 1.6 for the swollen spherical model, and half that value for an elongated model. <BR>
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But, that is quite a bit more work. To be honest, on the basis of the data you have to date, you might as well toss a coin. Only hint I can give is that natively unfolded proteins of low-ish molecular mass are pretty unusual things. See Uversky, V.N. (2002) Eur J Biochem <B>269</B> 2-12. So - if I was putting money it, I would go for an elongated shape !<BR>
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All best wishes for your work<BR>
<BR>
Arthur Rowe<BR>
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Arthur J Rowe<BR>
Professor of Biomolecular Technology<BR>
NCMH Business Centre<BR>
University of Nottingham<BR>
School of Biosciences<BR>
Sutton Bonington<BR>
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Tel: +44 (0)115 951 6156<BR>
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I had just analyzed a protein which has MW of 41.4 kDa from static LS<BR>
analysis (monomer 41.7kDa) and Rh=4.2nm from dynamic LS.<BR>
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What can I infer about the shape (beyond that it is not globular)?<BR>
Pointing to references appreciated. <BR>
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Thank you, Ewa<BR>
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