Hydrophobic Interactions
- Hydrophobic interactions are the most important noncovalent forces that will cause the linear polypeptide to fold into a compact structure. However, it is not the interactions between side chains of hydrophobic amino acids that induce the strong interaction, but the increase in entropy gained by the removal of hydrophobic surface area from ordered solvating water. The aggregation of the hydrophobic surfaces gives the tightly packed core of a protein. The hydrophobic interactions give a gain of 0.0-2.5 (1.5) kcal mol-1 per methylene group by removing approximately one-third of the ordered solvation water on formation of the secondary structure elements. On further folding into a tertiary structure another one-third of the ordered solvation water is lost.
- Hydrophobic interactions will not only be present between the amino acids with hydrophobic side chains, but between all residues depending on their total hydrophobicity. Not surprisingly the hydrophobic residues tend to cluster in the core and the hydrophilic residues on the surface. In proteins, the aliphatic side chains (Ala, Val, Leu, Pro), aromatic sidechains (Phe, Tyr, Trp), excluding the polar OH of Tyr and NE of Trp, and neutral sulphur containing sidechains (Cys, Met) are hydrophobic groups. These will take part in hydrophobic interactions and will try to fold into the protein cores.
Many different hydrophobicity scales have been developed to order the amino acids in terms of their propensity to form hydrophobic interactions. There are very many scales available. We have followed the most commonly used scale “Kyte & Doolittle's scale” published in the early 1980s.
This scale divides the amino acids as follows: The following residues are considered to participate in interactions if they fall within 5Å range.
ALA, VAL, LEU, ILE, MET, PHE, TRP, PRO, TYR.REFERENCES :
[1] http://pps00.cryst.bbk.ac.uk/course/section9/index.shtml
[2] kyte and doolittle’s scale.