[RASMB] frctional ratio

[Arthur Rowe]

Ewa -

I think the bottom line is that, without further experimentation, one can
only deduce that expectations of elongated conformation (based upon
sequence, perhaps ?) seem very plausible.

I entirely agree with John Champagne's point that working at 690 nm, even a
rod-shaped particle would behave more or less as an isotropic scatterer. An
expected dissymmetry ratio ball-parking at around1.02 or so does not sound
very hopeful !

All the best for any further work on your system

Arthur

Arthur and others,

thank you very much for responses.

I will look up the reference.

The protein is not glycosylated and it is expected to
be elongated, but I was wondering how much more can I
infer, so Arthur's comments were helpful since I have
plenty of it left so in a spare time.....

Yes, I had used DAWN for static (and dynamic from one
angle simultaneously) and cannot get Rg since the
protein is too small for when using 690 nm.

Thank once more, Ewa




--- Arthur Rowe <arthur.rowe at nottingham.ac.uk> wrote:
> 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
> 
> 
> --
>
*******************************************************
> 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
>             +44 (0)116 271 4502
> Fax:        +44 (0)115 951 6157
> email:      arthur.rowe at nottingham.ac.uk
>             arthur.rowe at connectfree.co.uk (home)
> Web:        www.nottingham.ac.uk/ncmh/business
>
*******************************************************
> 
> 
> 
> 
> 
> 
> 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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> 
> 
> 


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