From: Jose Garcia de la Torre <jgt@fcu.um.es>
  To  : lxs28@cac.psu.edu, rasmb@bbri.harvard.edu
  Date: Thu, 29 Apr 1999 18:05:59 +0200

Re: Diff. Coeff. of Dynamic protein

Dear Lumelle and RASMBers

Here is some feedback on Lumelle's question:

>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.

Determining internal mobility of a subunit/domain/etc from sedimentation 
coefficient will be possible only if the size of the mobile part is not
much smaller than the rest of the macromolecule. Otherwise the change in 
sedimentation coefficient would be too small.

>My thought
>was that a largely dynamic domain should increase the frictional
>coefficient and therefore decrease the diffusion coefficient. 


If the overall (average, due to flexibility) size of the macromolecule
in its 'flexible' state' is larger than that the one in the (hypothetically)
'rigid' state, then the frictional coefficient should increase. However, 
flexibility not always causes an increase in size; for instance, if a
flexible joint is induced in the middle of an elongated structure that 
would be straight in the rigid state, the mean size (for instance Rg) and
the friction coefficient would decrease and diffusion would increase.

> 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.

The doubt is reasonable - I have no immediate answer. Is it possible to
'frozen' the internal motions physically (temperature) or chemically
(pH,reagents,...)??? Measurements in two different conditions, both 
put in the form of s_0,20w could show some differences.

Best regards to all of you,
Jose Garcia de la Torre


-----------------------------------------------------------
Jose Garcia de la Torre

Departamento de Quimica Fisica     Phone: + 34 - 968 -367426
Universidad de Murcia              Fax:   + 34 - 968 -364148
30071 Murcia, Spain

WEB: <http://leonardo.fcu.um.es/macromol>
-----------------------------------------------------------