Is it possible, as I have heard about some DNA-binding proteins, that it is
at least partially intrinsically disordered (ID), which might change the
Stokes radius? You could cross-check by SDS-PAGE or SEC (ID's run larger).
CD, with careful protein quantification, might also do the trick. ID itself
might also change the dn/dc value, perhaps due to hydration (about that I am
not sure, though--I have read that this has an effect on PSV for AUC,
though).
Jacob
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
*******************************************
----- Original Message -----
From: "Engin Ozkan" <eoz...@stanford.edu>
To: <CCP4BB@JISCMAIL.AC.UK>
Sent: Friday, March 27, 2009 9:57 AM
Subject: Re: [ccp4bb] off topic - static laser light scattering
Dear Tassos,
Your assumptions are right, if (1) your dn/dc is accurate, or (2) your
machine is calibrated. We recently measured a protein of a similar size to
yours, and when a 700 Da ligand was added to the buffer, the measured
protein mass was increased accordingly. So MALS can be pretty accurate.
For our dn/dc, for pure proteins, we always use 0.185 (not 0.19). For
sugar groups, we assume a dn/dc of 0.14, and estimate a mass-averaged
value for the glycoprotein (usually somewhere between 0.175 to 0.18). For
DNA and RNA, the values will be different, again.
You may also realize that by changing a simple calibration constant, you
can modify your measured molar masses anyway you want. It may be time for
a recalibration (it is not difficult, you can do it yourself). We tend to
regularly run BSA, and see if everything is as expected with our
equipment.
Good luck,
Engin
Anastassis Perrakis wrote:
Dear all,
The MALLS instruments on-line with an FPLC and with an RI detector,
should provide an 'absolute MW', shape independent,
and indeed in our hands they do well. Until yesterday, where a 21kD
protein pretends to be 25 kD. We did the mass spec
anyway, and its 21kD as we expected to the residue, but I am still
puzzled by that result.
One central assumption for the MALLS formulas, is that dn/dc, the
specific refractive index increment, is constant for unmodified proteins,
made by aa with no sugars etc. Literature suggests dn/dc values for
proteins to be constant and between 0.189/0.190 is a good value,
with minimal buffer dependence for aqueous buffers with 'the usual'
salts.
I am a rather bad physicist, but my reading tells me that dn/dc, and thus
light scattering, depends to the "laser-light induced dipole in the
molecule". Is there any reason to believe that in theory a molecule with
a very particular charge distribution (eg a small DNA binding protein
which is already a 'dipole') would have significantly different dn/dc
values? Is anyone aware of such an experiment? Literature searches were
in vain ...
Best -
Tassos
