From: Arthur Rowe <Arthur.Rowe@nottingham.ac.uk>
  To  : lxs28@cac.psu.edu, rasmb@bbri.harvard.edu
  Date: Tue, 27 Apr 1999 10:39:53 GMT0BST

Re: Diffusion Coefficient with Dynamic info for a protein?

Lumelle -

Since the protein in question is big enough to have both outer and inner domains, 
it sounds as if NMR - the obvious choice - is out. So can you use sedimentation 
velocity ?

In *principle*, you could bead model the protein from its crystallographic structure 
(do you have it?) and see if the predicted friction is significantly smaller than the 
friction measured.  In practice, the uncertainty as to hydration is likely to render 
this method equivocal, unless you have a seriously big effect. 

My own suggestion would be a simple one. If there is outer domain flexibility, it is 
likely that the flexibility will be temperature-related.  So if you measure the s value 
accurately in the region 5 - 30 deg C, and correct it to standard conditions 
(SEDNTERP does it for you, including a correction for vbar-temperature 
dependence), and if you see a change, you may have an effect. Well - if its in the 
right direction.

Alternatively, if you have a DLS kit with temperature control, that needs no vbar 
corrections, although the other correction for viscosity does come in, and I guess 
that any change in RI increment too would affect things.

Of course, there would be no way of saying that any effect seen related to OUTER 
domains, but on the whole that would be more plausible than the other way round.

Arthur Rowe




Date:          Mon, 26 Apr 1999 14:44:07 -0400 (EDT)
From:          "Lumelle A. Schmiedekamp" <lxs28@cac.psu.edu>
Reply-to:      "Lumelle A. Schmiedekamp" <lxs28@cac.psu.edu>
To:            rasmb@bbri.harvard.edu
Subject:       Diffusion Coefficient with Dynamic info for a protein?



 A colleague in the department asked me if it is possible to determine not only 
shape information from sedimentation velocity, but also to determine the degree of 
dynamic movement of outer domains of a protein.  My thought was that a largely 
dynamic domain should increase the frictional coefficient and therefore decrease 
the diffusion coefficient.  However, without a rigid control protein of the same 
shape, I do not know how to measure this type of dynamic effect.  Any suggestions 
or ideas would be much appreciated. 

 Thanks. Lumelle 

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