Protein Structure and Function. Application of Bioinformatics Methods - John Rigden 2014

Bioinformatics methods for studying the structure and function of disordered proteins
Disorder prediction
Charge-hydropathy plots

The classical approach to assessing protein status regarding disorder is based on Uversky's observation that a combination of low mean Structure/106.html">Hydrophobicity and high net charge distinguishes IDPs from other Proteins. This principle is straightforward to apply by plotting net charge versus mean hydrophobicity (Uversky et al. 2000), either in charge-hydrophobicity coordinates or on a Uversky plot. On this plot, IDPs typically cluster in the region of high net charge and low mean hydrophobicity. They are separated from Globular proteins by a linear boundary defined by the formula <charge> = 2.743 * <hydrophobicity> - 1.109 (Fig. 5.1), which was determined with high precision in an earlier study (Oldfield et al. 2005a). A limitation of the charge-hydrophobicity plot is that it only provides binary Classification of Proteins without offering amino acid-level resolution. To overcome this limitation, Sussman and colleagues extrapolated this principle (Prilusky et al. 2005) by applying a sliding-window approach to the protein sequence to calculate mean hydrophobicity and net charge, thereby predicting per-residue disorder (FoldIndex, Fig. 5.2).