Hydrophobic bonds in proteins arise as a consequence of the interaction of their hydrophobic (i.e., "water-disliking") amino acids with the polar solvent, water. The hydrophobic amino acids are gly, ala, val, leu, ile, met, pro, phe, trp (see amino acid structures for reference). These aa's have hydrocarbon sidechains that, because of their non-polar chemistry, are forced into close association (hydrophobic "bonds") in an aqueous solvent. To understand the formation of hydrophobic bonds, familiarity with the energetics that drive the packing of solvent H₂O molecules into liquid lattices is required.

Liquid water molecules, at life-supporting temperatures, form groups (lattices) that are hydrogen-bonded networks ({H₂O}_20-30). Thermodynamic considerations tell us that the formation of these lattices arise as H₂O molecules attempt to optimize the number of energetically favorable H-bonds. Consider what happens, then, if hydrophobic, amino acid sidechains "poke" into the aqueous solvent. When this situation arises, shown below for two phenylalanine residues, the H₂O lattice is disrupted and H₂O molecules form a shell around the non-polar sidechains with which they cannot chemically interact. These H₂O's are unable to participate in H-bonding and lose freedom of movement, both of which are energetically unfavorable events.

Note: in the Chime figures below, only single planes of water shell molecules are shown, for ease of visulaization.

However, if the hydrophobic molecules are closely juxtaposed, shown below for the two phenylalanine sidechains, some H₂O molecules are "freed", allowing their participation in lattice formation. This is quite energetically favorable, and results in maximal association of hydrophobic molecules in an aqueous solvent, i.e. hydrophobic bond formation. The energetics of hydrophobic bond formation drives amino acids with hydrophobic sidechains into the interior of proteins, in most cases; this is a very important component of proper protein folding.

You may wonder about the effects of polar amino acids on H₂O lattices. Although they too disrupt lattice structure, they are able to electrostatically interact with the polar H₂O molecules that form shells around them (through H-bonds and ionic attractions). These electrostatic interactions help make up for the lost energy of H₂O lattice disruption.

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