Question

Biochemistry: I am doing a lab report on protein quaternary structures using a SDS-PAGE. We used denaturants such as BME and urea to see which proteins were held by disulfide bonds. The proteins that we used were Carbonic anyhydrase (CA), glyceraldehyde 3-phosphate dehydrogenase (GPD), hemoglobin (Hb), and superoxide dismutase (SOD). We had a set that was treated with BME and Urea. The other set was plain. Well, results were just awful. No I do not have the gel results on hand.

All I really want to know is which protein out of the 4 have disulfide bonds and which one do not? this will let me know which ones were affected by the denaturants and which ones weren't. How does the denaturants affect the proteins?

Answer 1

Among the proteins that you used Carbonic anyhydrase (CA), glyceraldehyde 3-phosphate dehydrogenase (GPD), hemoglobin (Hb), and superoxide dismutase (SOD), SOD has disulfide bond.

SOD have internal sulfur bonding...and it tends to aggregate under condition of promoting disulfide bond formation.

Generally in the human causes neural damage in amytrophic lateral sclerosis is yet poorly understood. A striking, as well as an unusual, feature of SOD is that it maintains intrasubunit disulfide bonds in the reducing environment of the cytosol.  we investigate the role of these disulfide bonds in folding and assembly of the SOD apo protein (apoSOD) homodimer through extensive protein engineering. The results show that apoSOD folds in a simple three-state process by means of two kinetic barriers: 2D⇌2M⇌M2. The early predominant barrier represents folding of the monomers (M), and the late barrier the assembly of the dimer (M2). Unique for this mechanism is a dependence of protein concentration on the unfolding rate constant under physiological conditions, which disappears above 6 M Urea where the transition state for unfolding shifts to first-order dissociation of the dimer in accordance with Hammond-postulate behavior.

Structural comparison of the SOD homodimer and monomer. (Left) Structure of the human SOD homodimer (1SPD), showing the positions of the cysteines, the loop containing residues 49–84, and the Cu and Zn ions. (Right) Loop displacements upon dissociation ...

Therefore, the SOD became denatured by the Urea experiment.. as it denature the disulfide bonds....