Answer to Question #68193 in Molecular Biology for Sanjukta Ghosh

Question

Two proteins of similar molecular weight (<900 Da), same net charge in the solution but with different amino acid composition is to be separated. Which one should be used?

a. Cation exchange b. Anion exchange c. gel filtration d. Reverse phase

My attempt:

Since the net charge is the same so there's no point using ion-exchange.

Gel filtration or Size exclusion rules out as the sizes are the same.

So the only thing left to be exploited is the hydrophobicity of the side-chain of amino acids.

I have a feeling that hydrophobic interactions are least in proteins, less no. of hydrophobic groups are to be found in one as compared to polar groups. So using reverse will be best because...

Well I think I'm missing out something. Aren't we suppose to decide the combination of stationary and mobile phases based on the component of analyte we want to elude at the end?