Subject: [Protein-analysis] Re: heterooligomer or homooligomer

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Subject: [Protein-analysis] Re: heterooligomer or homooligomer

Dr. Ulrich Wacker
Hi,
 
I would have a suggestion how to solve the heterooligomer/homooligomer problem in case that the sample fulfills the following prerequisites:
1. the protein complex originates from an organism with a fully sequenced genome.
2. the 200 kDa-gel filtration fraction already is reasonably pure.
3. the sequence has cleavage sites for trypsin (what many proteins in this MW-range will have)
In this case you could cut out the major bands either from 1D-SDS-PAGE or the major spots from a 2D-gel of this purified 200kDa-gel filtration fraction, digest the bands/spots using a suitable protease (trypsin?) and investigate all samples using MALDI-MS. In case of a homooligomer you should identify the same protein as the dominant protein in all samples. If you, however, find a different protein as the main constituent of one of these dominating spots you will have reason to believe that this is a heterodimer.
 
Ulrich
 
 

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