Size exclusion chromatography, also known as molecular sieve chromatography, is a chromatographic method in which molecules in solution are separated by their size and molecular weight.
Molecular weight of the protein was found to be 60 kDa by size exclusion chromatography. So, 60 kDa is the molecular weight of intact native protein.
6 M urea will denature the protein, that is protein will lose its secondary and tertiary structure, however its disulphide bonds will remain intact in the presence of urea. Urea does not reduce the disulphide bonds. Urea belongs to a class of compounds known as chaotropic denaturants, which unravel the tertiary structure of proteins by destabilizing internal, non-covalent bonds between atoms.
So when size exclusion chromatography was carried out in the presence of 6 M urea, 30 kDa species was obtained, it’s because, urea denatures the proteins, so subunits of proteins (each subunit 30 kDa) were separated from each other in the presence of urea.
However, when size exclusion chromatography was carried out in the presence of 6 M urea and Beta mercaptoethanol, a single molecular species of 15 kDa was obtained. It’s because, beta mercaptoethanol is a reducing agent. It reduces the disulphide bonds (that form between thiol groups of cysteine residues) present in the protein.
Each single 30 kDa subunit of protein was further made up of 2 single 15 kDa subunits that were held together by disulphide bond, which was reduced in the presence of beta mercaptoethanol.
Hence 60 kDa protein is a tetrameric protein held together by disulphide bridge.