Question

Together you and your lab parent prepared three aliquots of green fluorescent protein (GFP) that were all visibly fluorescent. You place one aliquot into a test tube containing a solution at pH2, the second aliquot into a test tube containing a solution at neutral pH and the third aliquot into a test tube containing a high concentration (6M) of guanidinium ions. After this you both observed that the second test tube was the only test tube that contained GFP that was still visibly fluorescent. Using your knowledge of the impact of pH and chaotropic agents on proteins explain why the protein present in the aliquots in the first and third tubes are no longer fluorescent.

Answer 1

At pH 2 , there is high concentration of H+ ions that made the protein positively charged that alters the H-bonding and salt bridge patterns and protein looses it's native confirmation and hence the flourescence activity as well.

Guanidium is a chaotropic agent that destabilize the protein structure by having favourable interaction with the protein. These molecules enter the hydration shell of the protein and disturb the H-bonding pattern and thus destroy the native confirmation of the protein .