A fourth weak force—a hydrophobic clustering force—also has a central role in determining the shape of a protein. As described in Chapter 2, hydrophobic molecules, including the nonpolar side chains of particular amino acids, tend to be forced together in an aqueous environment in order to minimize their disruptive effect on the hydrogen-bonded network of water molecules (see Panel 2–2, pp. 92–93). Therefore, an important factor governing the folding of any protein is
As a result of all of these interactions, most proteins have a particular three-dimensional structure, which is determined by the order of the amino acids in its chain. The final folded structure, or conformation, of any polypeptide chain is generally the one that minimizes its free energy.
Biologists have studied protein folding in a test tube using highly purified proteins. Treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together, unfolds, or denatures, a protein.
This treatment converts the protein into a flexible polypeptide chain that has lost its natural shape. When the denaturing solvent is removed, the protein often refolds spontaneously, or renatures, into its original conformation.
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