a Which amino acids affect the color yield for the Coomassie

a) Which amino acids affect the color yield for the Coomassie dye binding assay? (See Table 1-1, Experiment 1 in your lab manual). b) of bovine ribonuclease and rat fumarase, which would you expect to have a higher color yield in the Coomassie dye binding assay? Support your answer with calculations. (Remember to compare mole fractions of the relevant amino acids, not total residues

Solution

1. colour yield in coomassie dye-based protein assays associated with the presence of certain basic amino acids such as arginine, lysine and histidine in the protein. Van der Waals forces and hydrophobic interactions also participate in the binding of the dye by protein.

2. bovine ribonuclease has 18 basic amino acids corresponding to a mole fraction of 0.144 whereas rat fumarase has 65 amino acids whose mf is 0.131.

as per my knowledge, there is no effect of mole fraction in CBB binding. but high molecular proteins are visualised more and high concentration proteins with high basic amino acid content are detected with high sensitivity.

so rat fumarase which is about 54kDa should have high color than ribonuclease