From: Chin, Christopher <cchin@utmb.edu>
  To  : 'bgyjpaw@leeds.ac.uk' <bgyjpaw@leeds.ac.uk>
  Date: Tue, 12 Sep 2000 10:21:34 -0500

RNA vbar

Jonathan,

In reference to your previous question about RNA v-bar (4/6/00), I have not
seen any discussion in the Rasmb discussion board So I am giving my 2 cent
worth of suggestion in the hope that the experts in this field will voice
their opinions.  We know that for protein vbar, with known amino acid
sequence, SEDNTERP is the method of choice to obtain vbar. You can then
input in this calculated vbar value into the edited Sedimentation
Equilibrium curve (generated from the experiment) to get associated or
non-associate mass of the protein molecule weight with fairly good accuracy,
provided your protein sample is very pure.  But what happen if one works
with glycoprotein or DNA, (in your case RNA) and cannot get vbar from
SEDNTERP.  I have done some preliminary work using a backdoor approach in an
attempt to get vbar from macromolecule. I don't know if this approach will
work for small molecule like selenium or acetyl containing amino acids,
unless one can generate a decent sedimentation equilibrium curve, which is
the key for this approach, from AU.  I call this approach "vbar via back
calculation".
I believe this "Back Calculation" method will yield a realistic vbar value
for protein, glycoprotein, DNA. Perhaps it will work for RNA also(I have not
yet tried).
Provided the following conditions are met:
a. The sample is pure
b. The SE experiment data is accurate
c. The molecular weight is accurate
I think this approach works well with bona fide monomer or n-mer, but I
doubt if it works for monomer-dimer or monomer-nmer at equilibrium because
under such condition one will have difficulty inputting a correct apparent
MW to reflect the sedimentation equilibrium curve that was generated.

If you are interested in applying this approach to get your RNA v-bar, I
will be glad to send you the procedure describing how I use the following
Lamm's equation to extract v-bar from the sedimentation equilibrium curve. I
can also share my preliminary tabulated data (v-bar overview) with anyone
who would like to explore using this approach to obtain hard-to-get v-bar
values.



f=c0*exp((w*3.1416/30)^2*m*(1-v*p)*(x^2-x0^2)/(2*R*T))


-------------------------------------
Christopher Chin
Manager
Sealy Center for Structural Biology
HBC&G, 5136 MRB. rt1055 UTMB
cchin@utmb.edu, 409-772-1693, efax 708-585-1920
-------------------------------------