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similar size of proteins but different movement on SDS-PAGE


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#1 saad

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Posted 13 May 2011 - 06:57 AM

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.

Edited by saad, 13 May 2011 - 06:59 AM.


#2 bob1

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Posted 13 May 2011 - 04:36 PM

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.




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