The SDS converts them to their primary structure and binds to them to give them a uniform charge:molecular weight ratio, so they are seperated by their molecular weight rather than the charge that they would normally carry. FYI we didn't use SDS, and yes, I should have used proteins rather than enzymes, but it was late and I had been up for hours doing work.
I dont even know why I am replying to your post to be honest, what I replied with might be wrong but I have nothing to prove to you, I asked for people's help, not replies like that. I'll be the first to put up my hand and say I dont know something, like where to find the molecular weight of a protein for example, which is why I came on here asking the question.