The hydrophobic moment and its use in the classification of amphiphilic structures (review).
Amphiphilic alpha-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, <microH>, 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 alpha-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 <microH>. Taken with the window's mean hydrophobicity, <H0>, hydrophobic moment plot analysis uses the coordinate pair, [<microH>, <H0>] to classify alpha-helices as either surface active, globular or transmembrane. More recently, this latter analysis has been extended to recognize candidate oblique orientated alpha-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 alpha-helix structure/function relationships are considered.
Phoenix
David A
DA
Centre for Forensic Science, University of Central Lancashire, Preston, UK. daphoenix@uclan.ac.uk
Harris
Frederick
F
D000595:Amino Acid Sequence; D000818:Animals; D005583:Fourier Analysis; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D010507:Periodicity; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D013499:Surface Properties
D008565:Membrane Proteins