Proteins which run high on SDS-PAGE

Enrique Jose Labadan Frio - SCBC - 3421101 g3421101 at saturn.mahidol.ac.th
Fri May 10 23:29:54 EST 1996


Matt Parker (at332 at FreeNet.Carleton.CA) wrote:

: 	Thanks! Our proteins do have an unusually high amount of proline.
: Does anybody have any suggestions about why high proline content would
: cause the protein to run "large" on SDS-PAGE?

	Proline structurally constrains the main chain into a rigid
conformation (non-"linearizable" in the stretches where it occurs, if you
will) since it is strictly not an amino acid (imino acid for the purists)
and has a cyclic "side chain" (pyrrolidine, which is very constrained).
With the  principle of SDS denaturing the protein (how much is it really?
2-3 aa's perSDS moiety?) at sites where the psi/chi angles can rotate well
(all of the aa's at that, except proline), an insufficiently-"linearized"
polypeptide chain migrates slower (and thus higher on the gel) than one
with the same size but with fewer prolines. Look up any biochem textbook
for the structure.

	I'm still not clear though, on why proteins with some prolines
still migrate quite well... a lot of Pro's can make them significantly
slower, but for fewer ones, well... 

	All the best!

Querix
g3421101 at mucc.mahidol.ac.th

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