protein electrophoresis

doug feinstein dlfeins at UIC.EDU
Thu Sep 3 09:34:51 EST 1998

You might try including Urea in the gel. The presence of urea (between 2 to
8 M
) will cause distinct and different unfolding of the proteins than SDS alone.
In fact, depending upon the hydrophobicity, etc.. of the protein, the SDS may
not completely denature the protein. The mobility of the protein:sds comlex is
based upon the idea that the protein forms a cylindrical shape in comlex with
the SDS, which is coating the outside of the protein. hence, highly
regions will notallow the cylindrical shape to form. Similar conformatoin
dependent changes can occur due to phosphoyrlation, etc... I did these
sorts of
studies a long time ago, and have a paper in Analytical biochemistry around
1980 or so. 

34. Feinstein, D.L. and Moudrianakis, E.N.M. (1984) “Hydrophobic and Ionic
Effects upon the Electrophoretic Mobilities of the Subunits of Coupling Factor
1 from Mitochondria” Anal. Biochem. 136, 362.

You can also try Ferguson plots: this is to run the samples at different
acrylamide concenttrations, then plot the relative mobility versus the
acrylamide concentratoin. This slope and intercept of such plots gives you
informatoin about the conformatoin and net charge of your protein.

good luck
Douglas L. Feinstein's all in your mind.....
Associate Professor 
NeuroAnesthesia ReSearch
University of Illinois at Chicago
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