Branching stiffens large nonpolar side chains. The branched side chains of valine, leucine and isoleucine provide hydrophobic bulk yet limit internal flexibility. Stiff side chains are easier to fit into specific positions during the chain folding process. Valine, isoleucine, and leucine are almost always found in the interior of protein molecules. The branched-chain amino acids comprise a fourth of the amino acids in the proteins of human skeletal muscle, where they play key roles in protein structure and fuel metabolism.

Proline vs. Valine

For a side chain to be hydrophobic, it must have more than two carbon atoms and no polar groups. We'll discuss R-groups with aromatic rings later and focus on aliphatic hydrocarbon chains. Note that we jumped from Ala and Pro (both feel happy in either a nonpolar or polar environment) to the branched-chain amino acids, which are definitely hydrophobic. It is important to understand why Nature avoided straight hydrocarbon chains, such as ethyl or propyl, as R-groups.

A straight propyl side chain would be free to wave around in the solvent in an unfolded protein. The γ methylene group and the δ methyl group of a propyl side chain are free to rotate about the connecting C–C single bonds. Consequently, a propyl side chain in the unfolded protein would sweep out a large volume relative to the α carbon. During folding of the protein the propyl side chain would lose most of this freedom as it were packed into the hyrophobic interior. This large loss of side chain entropy during protein folding rules out the use of the propyl group as a side chain.

Now consider proline. The δ carbon of the "propyl" group is linked to the a nitrogen atom to form an imino group. This fuses the side chain to the backbone of the polypeptide chain, creating a rigid cyclic structure. Consequently, no loss of side chain entropy occurs during protein folding. Although the three carbon atoms are hydrophobic the highly polar character of the peptide group counteracts any tendency of the prolyl side chain to flee from water.

Branched-chain amino acids have either three or four carbon atoms in their side chains. However, the rotational entropy of the branched side chains is much smaller than that for a straight hydrocarbon chain with the same number of carbon atoms. For example, blocking the rotation of either γ carbon stops rotation of the valine side chain.