Oblique orientated alpha-helices and their prediction.
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.
Harris
Frederick
F
Department of Forensic and Investigative Sciences, University of Central Lancashire, Preston, UK.
Daman
Abel
A
Wallace
James
J
Dennison
Sarah R
SR
Phoenix
David A
DA
D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*
D011506:Proteins