From: Geoff_Howlett.BioChem@muwaye.unimelb.edu.au
  To  : rasmb@bbri.eri.harvard.edu
  Date: Sat, 20 May 1995 09:44:58 +1000

Re: sedimentation database

Hi RASMB people

I would like to thank Michael Jacobsen for stimulating the discussion on 
resources of potential use to the new generation of centrifugists.  I 
share the view that data on viscosities, densities, vbars and extinction 
coefficients would be very useful.  My sneek preview of the program being 
developed by Tom Laue, David Hayes and with more recent input from John 
Philo suggest this is going to be a wonderful new tool in this area.  

My contribution to the debate is along the lines of how many new 
scientists (graduate students etc) are measuring densities, viscosities, 
vbars and extinction coefficients and how long is it since some of the 
older ones (I can remember once.....) made these sort of measurements.  
What sort of standards need to be developed?  I believe it would be very 
useful to have available state-of-the-art procedures and advice from 
experts which would permit these measurements to be made with such 
precision it would provoke admiration by others.

Would anyone like to volunteer to write a few lines in this regard.
 
Questions I have in these areas include:

Densities   Is the Anton Paar density meter still the method of choice and 
have there been any developments with this technology?  Does anyone use 
pycnometers for these measurements?

Vbars    Traditionally vbars measurements have required lots of protein 
and a reliable method of determining concentration.  Can measurements 
using the U/C and solutions containing D2O/H2O match the precision of 
accurate density measurements?  Can the vbar of an oligonucleotide be 
predicted from the base composition and does the value depend a lot on 
solution condotions?
(Can anyone tell me how to type vbar with a bar over it in microsoft 
word?)

Viscosities  Does one still use a U-tube viscometer?  Are there commercial 
instruments which are reliable?  What are the best standards?

Extinction coefficients  Methods which have been described include 
estimating the extinction coefficient from the amino acid composition and 
OD of the denatured species, measurements at very low wavelengths, 
determination of the concentration using the U/C and interference optics 
(ie assuming a value for the specific refractive increment- this method 
tends to be used by ultracentrifugists) and measurements of concentration 
using aminoacid analysis and an internal standard.  I have left out dry 
weight determination although I appreciate this is the absolute standard.

With respect to the deposition of ultracentrifuge data.  I have less 
confidence this would be useful unless the goals were very clear and there 
was careful organisation and screening of suitable data.  I could 
certainly provide a few gigabytes from here but I don't imagine there 
would be a lot of euphoria re. its general usefulness. 

If I get any responses from the above questions I will summarise for the 
network.

Very best to all

Geoff Howlett