similar size of proteins but different movement on SDS-PAGE - (May/13/2011 )

Hi All

Actually I exprssed 6 differnt truncations from the same protein as a GST fusion proetin. These constructs were predicted to be unstrucured. After I purified the constructs ( the size between 32-35 kDa)and run them onto SDS-PAGE with the GSH beads two of them ran above 36 kDa and the others about or less than 31 (KDa Mark12 standard). I repeated the expreriment 3 times with the same results. Also there were some degradations.
Is it possible for those similar fragments of protein to run at different level/mass based on structure in denatured condition. Do the beads could affect the movements of proteins on Gel.
However, when I ran the pre and post induction samples all constructs seemed to run at similar size about 30/31 kDa.

any suggestions are highly appreciated.

Depending on the denaturing conditions and the sequence of the protein it is quite common for proteins to run at sizes different to those predicted. If you have a sequence that contains a lot of positively charged amino-acids it can run slower than predicted.