A two-component nucleation model of protein hydrophobicity.

ABSTRACT

A fundamental characteristic of soluble globular protein structure is a hydrophobic core and protein exterior comprised predominantly of hydrophilic residues. This distribution of amino acid residue hydrophobicity, from protein interior to exterior, has recently been profiled with the use of hydrophobic moments. The calculations enable comparison of the radial hydrophobicity distribution of different proteins and had revealed two features common to 30 proteins of diverse size and structure. One, a global feature, is the overall shape of the second-order ellipsoidal hydrophobic moment. The second, a specific feature, is a quasi-invariant hydrophobic-ratio of distances. Both features are dependent upon the rates of increase, from protein interior to exterior, of the accumulated numbers of hydrophobic and hydrophilic amino acid residues. These rates can be simulated simply with a two-component nucleation model of protein hydrophobicity. The model provides insight into the origin of the shape of the observed hydrophobic moment profiles and of the observed range of hydrophobic ratios. Consistent with observation, it is shown that a relatively wide range of hydrophobic and hydrophilic rates of increase yield a relatively narrow range of hydrophobic ratios. Furthermore, the model identifies one factor, the decrease in residue density with increasing distance from the protein interior, that is critical in providing the range of values that is comparable with the observed range.