[RASMB] Centrifugal force and protein dissociation

[Songpon Deechongkit]

Dear colleagues:

Currently, our lab has tried to determine the heterogeniety of an old
protein sample.  The protein, if folded correctly and behave well, should
remain tetrameric for a long time.  However, by sed. Vel. we found that
the protein sample is the mixture of monomer, dimer, and tetramer.  The
fit was done by DCDT (by John Philo).  Here are a few questions that I
would like to ask:

1)  Can centrifugal force tear multimeric protein apart?  This protein, in
particular, has a central channel where water can go through.

2)  If there is monomer-dimer-tetramer equilibrium, can we trust
sedimentation velocity data in terms of their relative amount?

3)  What is the reliability or error from the sed. Vel. fit?

We are very confused whether the fact that we observe
monomer-dimer-tetramer is true or is just an artifact.  I would greatly
appreciate your insight, thought, or suggestion in light of these
concerns.

Sincerely yours,
Songpon Deechongkit
PhD Candidate
Jefferey W. Kelly Lab
The Scripps Research Institute
La Jolla, California