From: Peter Schuck <pschuck@helix.nih.gov>
  To  : Stephanie Morris <smorris@medusa.bioc.aecom.yu.edu>
  Date: Tue, 31 Jul 2001 12:35:09 -0700

Re: small peptides

Stephanie,

We've had good experience with modeling numerical solutions of the Lamm
equation to data from the approach to equilibrium (i.e. a velocity
experiment at high speed extended to include scans close to equilibrium)
using SEDFIT.  Geoff Howlett, Cait McPhee and I have described the study of
peptides using absorbance data of the approach to equilibrium in Biophys.
J. (1998) 74:466-474.  In my experience, this works also very well with the
interference optics, even with molecules below 1 kDa.  

I agree with the previous comments that the baseline is a problem, but not
as much with the approach to equilibrium as compared to the analysis of
equilibrium data only, because of the additional information used on the
sedimentation process and the conservation of mass implicit in the Lamm
equation modeling.  (On the other hand, this introduces the position of the
bottom of the solution column as a new parameter that can sometimes be
slightly correlated, and as with other direct modeling of the sedimentation
boundary, a good fit is very important.)  Of course, it can get more
difficult when the peptides self-associate on the time-scale of
sedimentation, and I would probably run experiments at different
concentrations.  

Regards,
Peter

P.S. The newest version of SEDFIT can be downloaded from
www.AnalyticalUltracentrifugation.com (which is still under construction).


At 01:09 PM 7/26/01 -0400, you wrote:
>Dear RASMBers,
>
>I was wondering if anyone has performed sedimentation velocity or
>sedimentation equilibrium experiments on small peptides?  Recently, I
>performed a sed velocity experiment with a peptide that is about 2,000Da
>at a speed of 55,000rpm.  The boundaries were very broad and difficult to
>analyze using programs such as DCDT+ and SVEDBERG. Does anyone have any
>suggestions for running sed. velocity experiments using very small
>peptides and for analyzing this data?  I'm also interested in performing
>sed. equilibrium experiments with this peptide. Are there any quirks or
>helpful tips for running these kinds of experiments?  Any suggestions
>would be greatly appreciated.
>
>Thank you very much,
>
>Stephanie
>
>Stephanie Morris
>Albert Einstein College of Medicine
>1300 Morris Park Ave.
>Bronx, NY 10461
>smorris@aecom.yu.edu


***********************************************************
Peter Schuck, PhD
Molecular Interactions Resource
Division of Bioengineering and Physical Science, ORS
National Institutes of Health
Bldg. 13 Rm. 3N17
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Bethesda, MD 20892 - 5766
Tel: (301) 435-1950
Fax: (301) 480-1242
email: Peter_Schuck@nih.gov
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