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I have a protein gel and I'm comparing the reduced with the non-reduced gel. On the reduced gel, I have a few shorter bands but these bands appear with low intensity. In the non-reduced gel, I'm seeing more of the shorter product? What would case the protein to run "smaller" in the non-reduced conditions?

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By reduced and non-reduced gel, do you mean native PAGE under reducing and non-reducing conditions? Does your protein have any cysteins and is it known to form disulfide bridges? – Mad Scientist Mar 14 '12 at 10:47
SDS-Page and yes. – bobthejoe Mar 14 '12 at 17:12
So you're trying to run a denaturing gel? Strange, I've only seen protocols under reducing conditions for them, a denaturing gel under oxidizing conditions where disulfide bridges can form doesn't really make much sense. – Mad Scientist Mar 14 '12 at 17:18
You just remove the reducing agent. Its a pretty standard procedure and a quick search for non-reducing SDS-PAGE seems to show it. – bobthejoe Mar 14 '12 at 17:22
up vote 7 down vote accepted

The major effect of changing the redox environment of a protein is the formation or breakage of disulfide bonds. Under sufficiently reducing conditions no disulfide bridges will be present, while under oxidizing conditions your protein will form disulfide bridges if it has the ability to do so.

Disulfide bridges can significantly change the tertiary structure of a protein and change the behaviour of the protein on a gel that way. Generally, disulfide bridges should make the protein more compact and make it run faster on a gel.

It is therefore plausible that your faster band is the protein with disulfide bridges, which will appear to run like a smaller protein as it is more compact. The slower band then is the protein without disulfide bridges which can adopt a more extended conformation.

I'm assuming you're talking about native gels here, as denaturing gels usually contain DTT or beta-mercaptoethanol in the sample buffer to reduce any disulfide bonds and avoid this effect altogether.

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Just to add on to this answer, the reason we are able to measure protein size against a ladder with SDS-PAGE gels, reducing conditions and denatured proteins is because this treatment effectively linearizes all protein species in your samples. This make them well sorted by mass, rather than 3D conformation. – user560 Mar 16 '12 at 1:56

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