Introduction to Biochemistry - Quiz 2.2.2

If protein has many equally thermodynamically stable conformation, there wouldn't be a unique native fold.

The system of atoms is so huge that one can only simulate the fold of a few residues only, to predict the structure of a large protein is hard.

The native fold of the protein does not seems to have much correlation with temperature except in high temperature it denatures. So kinetic parameters doesn't seems to matter much.

The answer is the second choice - the most thermodynamically stable conformation is its native fold - this is essentially the thermodynamic hypothesis.

All of these are facts, but not all of them support the thermodynamic hypothesis, this two do:

RNase A regains activity when urea is removed - this means the protein can fold back to what it is by itself without help from anything else, and

We can predict the structure of some proteins based on sequence and knowledge of inter-molecular forces - this means protein molecules are just like any physical substances follow physical properties, there isn't any miracle about its fold - it just fold because of the law of Physics.

In high concentration urea - protein denatures. Beta-Mercaptoethanol is used to cleave the disulphide bond. (Disulphide bonds are bond formed between thiol group of two cysteine residues on the side chain). After all these bonds are cleaved, if we remove the urea by dialyzing it, it will become 90% active, however if we re-oxide the protein in the urea so that it forms the disulphide bonds randomly, the protein cannot go back to its native fold even after dialyzing. That is the Anfinsen experiment.

We see that first, protein spontaneously adopt their native fold after the urea is removed by dialyzing. Second, the disulphide bond should be formed after the folding complete, if not, the reoxided protein should also be able to get to the native fold, so we know the native fold specifies the location of the disulfphide bond, not otherwise.

B represents the native fold of the protein because it is the absolute minimum.
C represents a semi-stable folding immediate because it is a local minimum.