A major area of inquiry about protein structure has been the quest to understand how a globular protein folds into its characteristic shape. Much evidence indicates that the amino acid sequence plays a major role, because subtle changes in the sequence can easily change the secondary and tertiary structures of proteins.

Amino acid sequence - Secondary and tertiary structures can usually be destroyed (called denaturation) by heating a protein or changing the solvent environment (pH, salt content, organic content, etc.) in which the protein is dissolved. When the characteristic structure of a protein molecule in its physiological environment is lost, so too is the protein's normal function. If ribonuclease is heated to 80 C, it is converted from its normal, native state to a denatured state (Figure 6.20), which is unable to catalyze the cleavage of RNA. If the original physiological conditions are restored to ribonuclease, however, the activity and original structure of ribonuclease returns, indicating the molecule carries sufficient information in its amino acid sequence to properly fold itself. Though some proteins may need "help" in folding into the proper configuration, self-assembly of secondary and tertiary structures appears to be a general property of proteins.

Thermodynamic Factors - Folding is a thermodynamically favored process. Figure 6.22 helps illustrate the relative contributions to the free energy of folding of globular proteins.

Disulfide Bonds - Bonds between cysteine residues in a protein help to stabilize it once it has folded. Bovine pancreatic trypsin inhibitor (BPTI), which has 3 disulfide bonds in its 58 amino acid sequence, is one of the stablest proteins known. When the bonds are in place, it can be denatured at 100C only in very acid solutions. Removing one disulfide bond reduces its resistance to thermal denaturation considerably. Removing all of the disulfide bonds causes it to unfold at room temperature. If time is allowed for refolding and the disulfide bonds are reformed, virtually 100% of the original activity of BPTI can be recovered, indicating that the sequence of amino acids contains enough information to properly reestablish the folding of the polypeptide.