NATURE OF ACCESSIBLE AND BURIED SURFACES IN PROTEINS

The accessible surface areas were calculated for the individual residues in 12 proteins, and for the extended chains, the secondary structures and tertiary structure of 6 proteins. The formation of .alpha.-helices and .beta.-pleated sheets from an extended chain buries a greater proportion of polar surface than non-polar and gives 2-3 kcal/mol of hydrophobic free energy/residue. The surfaces buried between the secondary structures are very hydrophobic, being 2/3 non-polar and having more than 1/2 the polar part formed by groups that H-bond within their own piece of secondary structure or which are partially accessible to the solvent. As the 6 proteins increase in MW they bury an increasing proportion of their non-polar surface (60-79%) and a constant proportion of their polar surface (75%). The implications of these results for the theory of protein structure are discussed. An appendix shows that the accessible surface area of folded proteins is simply proportional to the 2/3 power of their molecular weight.