[RASMB] Can DCDT+ be used to detect small change in protein conformation? What is its limit?

[Chin, Christopher]

To John, all DCDT+ users and all interested colleagues, 
 
 John, I would like to have your comment in the following three experiments
using RNAseA as a model and DCDT+ as the method to do data analysis.
 
Experiment 1:  The purpose is to check the stability of RNAseA. The
comparison is made between the protein left at room temperature for a couple
of days and that storage in the freezer.
Experiment 2:  Question: Can the denatured RNaseA (has 4 s-s bond) in GuHCl
be refolded back to its native state in the absence of reducing agent?
Experiment 3:  Question: Can the denatured RNaseA (has 4 s-s bond) in GuHCl
be refolded back to its native state in the presence of reducing agent  TBP
(Tri-n-butylphosphine).
 
The major issue here is how I can differentiate the DS<?xml:namespace prefix
= o ns = "urn:schemas-microsoft-com:office:office" /> difference due to scan
chosen from the DS difference due to real experimental finding (between the
control and the sample).
 
I am pleased to say that, using the criteria that I have stated, e.g.
maximized or magnified the DS difference due to scan chosen (use a smaller
number for denominator when converted to %), minimized or play down the DS
difference between the control and the sample (use a larger number for
denominator when converted to % ), the results are pretty much I have
expected.  Do you think I try to push the instrument limit too far to obtain
these results by manipulating the treatment of data? 
 
s20,w values reported here are the results of fitting dcdt.
 
Thank you in advance for your comment or advice.
 
Chris
  

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Christopher Chin 
Manager, XLA-Analytical Ultracentrifugation facility 
Sealy Center for Structural Biology 
HBC&G, 5.134 MRB.UTMB, Galveston,TX 77555-1055 
cchin at utmb.edu, 409-772-1693, efax 708-585-1920 
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