Question

A protein is purified using ultracentrifugation and found to have a mass of 300 kDa. It is further separated on SDS-PAGE and is found to have a single band corresponding to a mass of 100 kDa. When the protein is treated with beta-mercaptoethanol (breaks disulfide bonds), the SDS-PAGE shows 2 bands, one at 20 kDa and one at 80kDa. Describe the tertiary and quaternary structure, include forces holding the protein together (Hint use prefixes like homo- or dodeca-)

So far the only answer I am able to come up with is that it is held together by hydrogen, and disulfide bonds. I think it is a hetro-trimer. Please explain the answer. Thank you.

Answer 1

In SDS -PAGE electrophoresis, SDS which is an anionic detergent is used that usually denatures the protein by breaking the bond between the subnits of secondary proteins that are usually made up of non covalent bonds such as hydrogen bonds, ionic bonds,They do not break the disulphide bonds which are a part of the tertiary and quaternary structure of the proteins.

So,in SDS PAGE, as single band is seen. but when protein is treated with β-mercaptoethanol,two bands are seen one at 20kDa and one at 80kDa. β-mercaptoethanol, is able to break the disulphide bonds between the protein subunits.This means that the 20 subnuit of proteins is attached to the 80 subunit of the protein via disulphide bond and when protein is treated with β-mercaptoethanol,this disulphide bond is broken resulting in dissociation of the subunits from each other and two bands are seen.

Tertiary and quaternary structures of proteins are formed by irregular folding of the peptide chains in three dimensions.The interactions in both tertiary and quaternary proteins consists of hydrogen bonds between polar R groups,hydrophobic interactions between non polar R groups, ionic bonds between charged R groups and covalent disulfide bonds between cysteine aminoacids on two different polypeptide chains.