[RASMB] upper concentration limit AUC

Mon Sep 8 05:51:38 PDT 2008

Hi Everyone

You are absolutely right, Tom. It is indeed more than a bit inelegant to mix
things up like this.

The trouble is that translational diffusion is itself is a mixed-up
phenomenon in which the driving force is thermodynamic, whereas the opposing
force is hydrodynamic. But maybe if we deal with it all on a
phenomenological basis, it should be possible to describe the situation in
high concentration SV? Given the fact that this latter is no more 'mixed up'
than the treatment of diffusion itself is, by its very nature?

What else to do? Send the Universe back for re-mastering?

Regards to all

Arthur

Hi-
Food for thought and a serious question.
The "natural" concentration units for k(s) are volume fraction (since it
is a hydrodynamic term).
The "natural" concentration units for k(D), or k(P) in Arthur's
discussion, are mole fraction (since it is a thermodynamic term).
Because of the different "natural" concentration units, is there a
fundamental difficulty in using sedimentation velocity to analyze high
concentration solutions?
Best wishes,
Tom

Arthur Rowe wrote:
>
>     Hi Christine (and everyone)
>
>     I think this discussion is already in the RASMB Archives.
>
>     To summarise very briefly, k(D) is indeed lower than k(s), but not
>     hugely so. For simple, spherical particles, defining all
>     coefficients in volume fraction terms and at limiting infinite
>     dilution, we can write
>
>     k(D) = k(P) - k(s) where k(P), the concentration dependence of the
>     chemical potential which is the force driving the flux in
>     translational diffusion, and is given for s single component by
>     (2BM + higher terms) where B is the 2nd virial coefficient. For
>     spheres, 2BM = 8 ml/g; k(s) = 4* ml/g:  so k(D) = 4 ml/g. I am
>     afraid that neglecting k(D) is not a good approximation.
>
>     Kind regards - will be seeing you (Christine) and lots of others
>     in Newcastle this week.
>
>     Arthur
>
>     *see "The sedimentation rate of disordered suspensions"  Brady,
>     John F.; Durlofsky, Louis J.
>     Physics of Fluids 1988 31 717-727 for the last word from the fluid
>     mechanics people. You can also look up my Chapter in the 1992 Book
>     (the 'black book') ed s Harding, Rowe & Horton) for details of my
>     own derivation. Which happens to be in total numerical agreement
>     with the Brady/Durlovsky treatment, right p to 64% volume fraction
>     . . . . .
>     *Note: *the value given above for k(s) = 4 ml/g is for *DYNAMIC
>     k(s)*. The usual measured value which gets reported is the
>     *KINEMATIC* k(s), which for spheres has the value 5.0 ml/g. You
>     can get either value out of theory, depending how you play it.
>     Brady & Durlovsky report the kinematic value. All of which was
>     first noted by Burgers in 1939/40, and has been much ignored ever
>     since! As no density 'correction' is called for in the estimation
>     of k(D) or of k(P), it seems reasonable to use the dynamic k(s) in
>     the equation above.
>
>
>     Dear Joris, dear all,
>
>     This reference may be perhaps useful.
>
>
>
>     Solovyova A., Schuck P., Costenaro L., Ebel C,
>
>     Non-ideality by sedimentation velocity of halophilic malate
>     dehydrogenase in complex solvents,
>
>     (2001) /Biophys. J,/ 81 1868-1880.
>
>
>
>     In this work, we analyzed sedimentation velocity profiles
>     considering hydrodynamic and thermodynamic non ideality. (i.e.
>     concentration dependency of s and D) in the case of an
>     homogeneous  solution of our protein of interest. The modified
>     Lamm equation was implemented in a model of analysis in Sedfit
>     (note that, unless the programme was recently modified, the kS and
>     kD are expressed in signal unit in sedfit)
>
>     From my experience, the sedimentation velocity profiles are
>     essentially modified by the concentration dependency of the
>     sedimentation coefficient. Thus the concentration dependency of D
>     can be neglected in a first approximation. Also from a theoretical
>     point of view, kD is much lower that ks.
>
>     All the best
>
>     Christine
>
>
>     Christine EBEL
>
>     Institut de Biologie Structurale CEA-CNRS-UJF
>
>     41 rue Jules Horowitz, F-38027 Grenoble France
>
>     Tel (33) (0) 4 38 78 95 70; Fax (33) (0) 4 38 78 54 94
>
>     christine.ebel at ibs.fr
>
>     http://www.ibs.fr/content/ibs_eng/presentation/lab/lbm/ebel.htm
>     -----Message d'origine-----
>     *De :* rasmb-bounces at rasmb.bbri.org
>     [mailto:rasmb-bounces at rasmb.bbri.org] *De la part de* Beld, Joris
>     *Envoyé :* lundi 1 septembre 2008 15:24
>     *À :* RASMB at rasmb.bbri.org
>     *Objet :* [RASMB] upper concentration limit AUC
>
>
>
>     Dear all,
>
>
>
>     A colleague asked me whether analytical ultracentrifugation has an
>     upper limit with regard to the concentration of the protein. They
>     want to measure the protein at the same concentration as the NMR
>     experiments (> 1 mM). I am not entirely sure but I thought this
>     should be no problem. One could easily measure off-peak at another
>     wavelength than 230nm, e.g. 235nm or 280nm, right?! Or does one
>     run into non-ideality phenomena when doing sedimentation
>     equilibrium at these high protein concentrations?!
>
>     Thanks a lot in advance for any feedback.
>
>     Best wishes,
>
>
>
>     Joris Beld
>
>
>
>     Hilvert Group
>
>     ETH Zürich
>
>     Switzerland
>
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-- 
Department of Biochemistry and Molecular Biology
University of New Hampshire
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Phone: 603-862-2459
FAX:   603-862-0031
E-mail: Tom.Laue at unh.edu
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