[RASMB] time to reach equilibrium

lelj lelj at interchange.ubc.ca
Fri Jun 6 17:41:00 PDT 2003


Hello everybody,

I have been reading very carefully all the email you sent about slow equilibration and also about the use of c(s) in the sedfit program.
And I have the following questions:

I work with a protein that definitively oligomerizes and in a bigger assembly than just dimer or tetramer. 
I did a number of velocity exp. at different speeds my problem is that I can only use the c(S) fit in sedfit because:
1)None of self association model is "big" enough for my system
2) I don't have the K valuse (I tried to solve the problem with equilibrium experiments first but then I went to the velocity)

I understand From your emails That I cannot use this model for a self-associating system (by the way, I see a major broad peak around the s I expect but also a number of small peaks at higher s)
What model should I use?
also, I tried to fit my vel.exp with the Van Holde- Weischet model of the beckman softwere and I see a weird behave: the middele poing are a "straight" line but at both ends of this straight vertical line the points deflect towards smaller value of s (almost like a C with the opening pointing to the left!) What does it mean?

Regarding the slow equilibrium:
To make sure that the system reached equilibrium I would almost be tempted to spin for longer times, but isn't there the risk to pellet at the bottom of the cell some large oligomer and loose information?

thanks to all
barbara

PS I can't wait to be at the UConn workshop... I have so many more questions to ask!!!!!


Barbara Lelj Garolla Di Bard
Dr. Mauk's Lab
Dept. of Biochemistry and Molecular Biology
University of British Columbia
2146 Health Sciences Mall
Vancouver, B.C. V6T 1Z3
Phone: (604) 822-2526





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