From: Diane Wakeham <wakeham@itsa.ucsf.edu>
  To  : rasmb@alpha.bbri.org
  Date: Mon, 11 Sep 2000 18:04:16 -0700

MW Determination for Rod- Shaped Protein(Axial Ratio?)

I am a rather inexperienced user of an XL-A analytical ultracentrifuge
to assess the assembly state of a highly nonspherical protein (approx
dimensions 115 x 28 x 24 angstroms, essentially rod shaped and rather
large) likely to form dimers or possibly tetramers.  Using the simplest
fits to my sedimentation equilibrium data with Optima software the
molecular weight I obtain is about 10- 20 kD less than I would expect
the actual protein size to be.  I checked the weight using mass spec to
confirm that this was not due to degradation of the sample.

I have many questions:  (1) Is it possible for molecular shape to affect
the parameters this much (2) What software do you recommend (preferably
free?) to fit this nonspherical data with?  (3) Is there are a software
package available to estimate the axial ratio, from estimated size
parameters or from a crystal structure?  (4) Is there a tutorial or any
literature for background on working with highly nonspherical molecules
using AUC?

 I tried to simulate the size using Ultrascan but found that it can't
handle an axial ratio lower than 6.  If I divide the two largest
dimensions in half as a crude estimate of radius for the axial a and b,
my ratio is closer to 4.  Your input would be very useful as I assess
how to interpret this data.

Thank you,
Diane Wakeham