[RASMB] Protein Self-Association, can we all agree on the same model?

[Chin, Christopher]

Happy New Year to you all.

 

If you are interested in doing protein self-association modeling
exercise, this is for you.

 

The XLA raw data set are provided here. The rule is simple. You can use
any of your favorite software to come up with a plausible model. The
goal is to see if people performing this exercise, using one's favorite
software, will the the same model (picture) emerge? If not, why not?

 

Last Christmas I encountered this interesting protein. The protein
sequence is known. It is about 91 KD for the monomer. Also the EM
picture is available.

 

The protein is in 25 mM HEPES, 0.1mM EGTA, 200mM KCl.

I ran SV (30K speed) and SE (7K and 8.5K speed) experiment at 4C. Fresh
samples were used for each experiment.

For analysis I used v-bar=0.7167, rho=1.0084, viscosity=1.0064E-2 (all
values are obtained from SEDNTERP but contributions from HEPES and EGTA
were omitted)

To get the apparent MW, I used scan 7 from the SE experiment and
selected subset radius ranges from ~6.9cm to 7.12cm.  I then
subsequently used the same radius range for self-association model
fitting to make the modeling comparisons more meaningful and more
consistent. 

 

For SV data analysis, I used SEDFIT and used all 186 scans for analysis.
I also used SEDNTERP to convert S4c,w to S20c,w. 

  

For SE data analysis I used SEGAL and SEDPHAT and also Origin to get a
ballpark value for the apparent molecular weight.  I took a look at scan
7 (20 hours) and also scan 10 (26 hours) for the 7K speed. I also took a
look at scan 15 at 8.5K speed.  

 

For model fitting I chose scan 7 from the SE experiment and selected
subset radius range from ~6.9cm to 7.12cm.  I used Beckman's Original
software to perform modeling analysis and used variance (goodness of
fit) as a guide to reach my conclusion.

 

I posted my data analysis and fitting results after the raw compressed
data set, in case you are interested in comparing the model that I came
up with using Beckman Origin 4.1 software.

 

 

Have fun!

 

With warm regards,

 

Chris

 

 

 

 

-------------------------------------------------------------

Christopher Chin

Manager

Sealy Center for Structural Biology

HBC&G, 5134 MRB. rt1055

UTMB cchin at utmb.edu <mailto:cchin at utmb.edu> , 

409-772-1693, efax 630-604-3416

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