Hydrophobic moments and protein structure

Abstract

The structure of a protein can be analysed in terms of what may be called the “hydrophobic moments” of (1) the entire molecule and (2) of the segments of secondary structure that make up the polypeptide chain. The zeroth moment is defined as the sum of the hydrophobicities of the amino-acid residues of the structure under consideration; it is the analogue of the net charge of a cluster of point charges. The first moment, or hydrophobic dipole moment, is the analogue of the electric dipole moment of a cluster of charges. Just as the electric dipole moment measures the asymmetry of the charge distribution, the hydrophobic dipole moment measures the amphiphilicity (asymmetry of hydrophobicity) of the structure. A large hydrophobic dipole moment indicates that a structure is predominantly hydrophobic on one side and predominantly hydrophilic on the other. A quadrupole hydrophobic moment may be similarly defined. It indicates whether a protein is more hydrophobic in its interior (as for a globular protein in aqueous solution) or at its surface (as for a membrane protein).