From: Jacqui Matthews <j.matthews@biochem.usyd.edu.au>
  To  : RASMB@bbri.org
  Date: Wed, 03 Nov 1999 14:57:12 +1100

cavities

Dear RASMBers

I have been performing sediemtation equilibrium experiments on a protein
which has a large cavity at the centre, which apparantly not accesible to
the solvent.  Based on the crystal structure, this cavity contains a number
of well-ordered waters.  If I calculate vbar based on amino acid
composition and cofactors, the apparant molecular weight I obtain is
consistently and significantly lower than expected (having tried out a
number of different conditions including different salt concentrations).
I am about to see if I can account for this difference by a) including the
ordered waters in my vbar estimations and b) assuming a completely
water-filled cavity.

Does anybody have any experience with thsi type of phenonemon?

I should add that it is impractical to determine the vbar for this protein
using densiometric techniques.

regards

Jacqui




**************************************************
Dr Jacqui Matthews
U2000 Fellow
Deparment of Biochemistry
Building G08
University of Sydney
NSW 2006
AUSTRALIA

Ph +61 2 9351 6025
Fax +61 2 9351 4726