I performed NATIVE gel electrophoresis and SDS PAGE electrophoresis for my porcine skin tissue ECM extracts. interestingly, I saw higher molecular weight protein bands in the case of SDS PAGE but didn't see any bands on the Native gel. why did that happen?
The denaturation process, which enables these proteins to be distinguished solely by size, is probably responsible for the greater molecular weight protein bands you saw in the SDS-PAGE. However, because of their size, structure, or interactions with other molecules, these same proteins might not migrate as well in NATIVE PAGE, which would leave no visible bands.
Yes, what Syed said is likely. Your proteins may remain in the well instead of entering the gel because they are not extracted from your sample or they are not separated from each other and are therefore too large.
What is your gel percentage in native-PAGE and used gel chemistry? I suggest trying BN-PAGE to overcome the migration differentiation...Cover the proteins with negative charge using coomassie stain and hope to get a similar pattern with SDS-PAGE. Compare the proteins by only their shape and size, not by charge-induced mobility variation...
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