Hydrophobic Interactions in Proteins


Proteins fold spontaneously into complicated three‐dimensional structures that are essential for biological activity. Much of the driving energy for this folding process comes from the hydrophobic effect, i.e. the removal of nonpolar amino acids from solvent and their burial in the core of the protein.

Keywords: folding; non‐polar; water; amino acid

Figure 1.

Sketch of the backbone structure of the protein methionine aminopeptidase from Escherichia coli. The chain begins at the amino‐terminus (N), includes 264 amino acids, and ends at the carboxy‐terminus (C). The protein includes α helices and β sheet strands as well as two metal ions (spheres) at the active site. Reprinted from Bazan JF et al. (1994) Proceedings of the National Academy of Sciences of the USA 91: 2473–2477, figure 2.

Figure 2.

Relationship between the hydrophobicities of the amino acids and the solvent‐accessible areas of their side‐chains. Reprinted and adopted from Chothia C (1974) Nature 248: 338–339, figure 1.

Figure 3.

Loss of protein stability, ΔΔG, for a series of leucine‐to‐alanine substitutions within T4 lysozyme. ‘L99A’, for example, denotes the mutant in which leucine 99 is replaced by alanine. Mutations that result in cavities of the largest volume cause the greatest loss of stability. At a cavity volume of zero, the loss of stability can be attributed to the difference between the hydrophobicity of leucine and alanine. Reprinted and adapted from Xu J et al. (1998) Protein Science 7: 158–177, figure 17A.


Further Reading

Creighton TE (1992) Protein Folding. New York: WH Freeman.

Richards FM (1991) The protein folding problem. Scientific American (January 1991), pp. 54–63.

Matthews BW (1996) Structural and genetic analysis of the folding and function of T4 lysozyme. FASEB Journal 10: 35–41.

Pace CN, Shirley BA, McNutt M and Gajiwala K (1996) Forces contributing to the conformational stability of proteins. FASEB Journal 10: 75–83.

Eriksson AE, Baase WA, Zhang X‐J et al. (1992) Response of a protein structure to cavity‐creating mutations and its relation to the hydrophobic effect. Science 255: 178–183.

Xu J, Baase WA, Baldwin E and Matthews BW (1998) The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect. Protein Science 7: 158–177.

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Matthews, Brian W(Apr 2001) Hydrophobic Interactions in Proteins. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0002975]