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

Bioinformatics methods for studying the structure and functions of disordered proteins
Properties of IDP sequences
Unusual amino acid composition of IDPs

Modern Methods for predicting disorder rely on various principles. Nevertheless, IDPs share certain common properties—namely, an Amino Acid Composition and sequence that distinguish them from ordered Proteins.

Uversky et al. (2000) and Dunker et al. (2001) were the first to note that the frequencies of occurrence of various Amino Acids in intrinsically disordered proteins differ markedly from those in ordered proteins. These differences are independent of the methods used to assign a protein to a structural group, as such proteins are consistently depleted in amino acids with low flexibility (hydrophobic amino acids) and enriched in amino acids with high flexibility (polar and charged amino acids). The former group (Trp, Cys, Phe, Ile, Tyr, Val, and Leu) is referred to as order-promoting amino acids, whereas the latter (Ala, Arg, Gly, Gln, Ser, Pro, Glu, and Lys) is termed disorder-promoting amino acids (Dunker et al. 2001). Similar trends have been reported in other studies (Uversky et al. 2000; Tompa 2002). It is now widely accepted that two primary features dictate protein disorder: a low overall Structure/106.html">Hydrophobicity, which precludes The formation of a stable globular core, and a high net charge, which promotes an expanded structural state through electrostatic repulsion.