The hydrophobic moment and its use in the classification of amphiphilic structures (Review)

Abstract

Amphiphilic &#102 -helices play a major role in membrane dependent processes and are manifested in the primary structure of a protein by the periodic appearance of hydrophobic residues. Based on these periodic sequences, the hydrophobic moment was introduced, <µ H >, which essentially treats the hydrophobicity of amino acid residues as a two-dimensional vector sum and provides a measure of amphiphilicity within regular repeat structures. To identify putative amphiphilic &#102 -helix forming sequences, hydrophobic moment analysis assumes an amino acid residue periodicity of 100° and scans protein primary structures to find the 11-residue window with maximal <µ H >. Taken with the window's mean hydrophobicity, < H₀ >, hydrophobic moment plot analysis uses the coordinate pair, [<µ H >, <H₀ >] to classify &#102 -helices as either surface active, globular or transmembrane. More recently, this latter analysis has been extended to recognize candidate oblique orientated &#102 -helices. Here, the hydrophobic moment is reviewed and data to query the logic of using a fixed window length and a fixed residue angular periodicity in hydrophobic moment analysis are provided. In addition, problems associated with the use of such analysis to predict &#102 -helix structure/function relationships are considered.

• Hydrophobic Moment
• Amphiphilic Alpha-HELIX
• Surface Seeking
• Transmembrane
• Oblique Orientated