[RASMB] frctional ratio

[Arthur Rowe]

Dear Ewa

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 = 1.83. 

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:

(1) you have one of these 'natively unfolded' proteins, whose normal state
is a loosely structured swollen one, or

(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)

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.

If - and its a big IF - you have enough material and the kit to hand to do
an intrinsic viscosity and 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.

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 269 2-12. So - if I was
putting money it, I would go for an elongated shape !

All best wishes for your work

Arthur Rowe


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Arthur J Rowe
Professor of Biomolecular Technology
NCMH Business Centre
University of Nottingham
School of Biosciences
Sutton Bonington
Leicestershire LE12 5RD   UK

Tel:        +44 (0)115 951 6156
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email:      arthur.rowe at nottingham.ac.uk
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I had just analyzed a protein which has MW of 41.4 kDa from static LS
analysis (monomer 41.7kDa) and Rh=4.2nm from dynamic LS.

What can I infer about the shape (beyond that it is not globular)?
Pointing to references appreciated.

Thank you, Ewa

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