[RASMB] Small peptides and AUC

[Scott David]

Hello All,
Following on from discussions of 90 % DMSO,etc. There are more
applications (at least through the NCMH) to look at peptides in
membranes and detergents, and talking to people in the AUC field, this
is a somewhat growing field as people become less fearful of
membrane-bound stuff. At this juncture I think it would be good if we
could start a discussion strand of what to watch out for when analysing
these samples. Original references very welcome.

Here's several very obvious things to get us started.

1) vbar. The bouyancy of the peptide changes with binding of lipids and
detergent. This has to be either (a) matched out by having a solvent
that has the same density as the lipid/detergent or (b) calculated from
the density increment. I also had a referee once ask me years ago
whether I had corrected for charge on a small peptide. The answer was
"no" as the peptide was actually a reasonably sized protein, but the
original reference for this would be good.

2) Speed. Peptides are small, you will need probably the highest speed
possible to analyse them, and for the XL-A/I that's 60K and the
associated problem of buying the correct centrepieces (Aluminium or
SpinAnalyticals SedVel60K). 

3) Co-sedimentation of the solvent. Peptides are small, therefore have
low S values. I seem to recall that Na+ sediments at around 0.3 S,
therefore you will need to think about how the sedimentation of your
solvent components affect the sedimentation of your sample. Not trivial
if these affect the solubility and stability of your peptide.

4) Small S values. Are our algorithms good enough?


Enjoy!

Dave.



Dr. David J. Scott
Lecturer in Physical Biochemistry
National Centre for Macromolecular Hydrodynamics
School of Biosciences
University of Nottingham
Sutton Bonington Campus
Sutton Bonington
Leicestershire
LE12 5RD
United Kingdom
dj.scott at nottingham.ac.uk
www.nottingham.ac.uk/ncmh
+44 (0) 115 951 6221 Phone
+44 (0) 115 951 6142 Fax


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