why we do native gel electrophoresis and what is the meaning of aggregation?

Question

what is the difference in the result we get from native and sds page.

thanks

Answer 1

an SDS-page denatures the protein, meaning proteins are largely separated simply based on molecular weight. If you want to prove that your protein is pure, you can run an SDS-page gel. If you have one band, you supposedly only have on thing in solution. You can confirm that it is your protein with other techniques such as mass-spectrometry, but all you can tell is that you have something of a certain (approximate) molecular weight, or more than one thing.

In a native gel, the proteins are not denatured; they are still the same well-folded structure. Let's say you wanted to show that your protein bound DNA. You could run a native gel. In one lane you have your protein, in the second lane you have your protein plus the DNA it binds, and in the third lane you would have your protein and a piece of DNA that based on the sequence it shouldn't bind. You should see the protein band be the same in the first and third lane, but a shift in the second lane. This proves that they bind. In the SDS-page gel, since the protein is denatured (unfolded) you would never see such a shift.

Your next question should then be "since native gels give more information, why don't people just run those all the time"--they're harder. So if all you want to show is that your protein is pure (or not) an SDS-page gel is easier and faster.

Lastly, about aggregation: when you conentrate proteins beyond their normal concentration in cells they can aggregate: clump together, potentially unfold, and precipitate as an insoluble mess. Since in a native gel all the proteins are running together very closely to each other, they are at a very high local concentration, and therefore are very prone to aggregation. This is the primary danger of native gels, and why they're not run very commonly. In an SDS page gel they're already completely unfolded and their attraction to the SDS is greater than to each other so they don't aggregate.

Answer 2

The first answerer looks like he got the electrophoresis right so I'll just tell you about aggregation.
Aggregation basically means when the protein clumps together(forming aggregates). It is caused by particles being attracted to each other. There are a number of different possible causes for example complementary charges can be used to attract each other. It can be caused by hydrophobic interactions e.g. if you put a hydrophobic protein into a hydrophillic solvent.

Answer 3

That sounds well complicated.