title: Oblique orientated alpha-helices and their prediction.
abstract: Oblique orientated alpha-helices possess hydrophobicity gradients, which allow the parent alpha-helices to penetrate the membrane at a shallow angle, thereby destabilising membrane lipid organisation and promoting a range of biological processes. These alpha-helices occur in a variety of membrane interactive proteins and a number of techniques have been developed to guide their identification using sequence data alone. Hydrophobicity profiling, which provides a one-dimensional analysis of sequence data, identified only 30% of known tilted peptides in a control dataset and was thus of limited predictive use. In contrast, extended hydrophobic moment plot methodology and amphipilic profiling which take residue distribution into account and provide two-dimensional analysis of primary structural data, were found to be good indicators of tilted peptide structure. Amphiphilic profiling identified 67% of tilted peptides in the control dataset and showed that potentially, approximately 40% of transmembrane alpha-helices possess tilted peptide structure. However, it has been shown that extending these simple methods to take into account the three-dimensional spatial distribution of residues gives no clear additional benefit to identifying tilted peptides.
authors.affiliation: Department of Forensic and Investigative Sciences, University of Central Lancashire, Preston, UK.
authors.forename: Frederick
authors.initials: F
authors.lastname: Harris
authors.forename: Abel
authors.initials: A
authors.lastname: Daman
authors.forename: James
authors.initials: J
authors.lastname: Wallace
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Dennison
authors.forename: David A
authors.initials: DA
authors.lastname: Phoenix
mesh_terms: D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins