Protein Structure and Function: Applications of Bioinformatics Methods - John Rigden 2014

Bioinformatics Methods for Studying the Structure and Function of Intrinsically Disordered Proteins
Properties of IDP Sequences
IDP Sequence Patterns

All the aforementioned studies, as well as the subsequent success of simple prediction algorithms based on amino acid propensity, indicate that the Amino Acid Composition is the primary factor determining structural disorder. However, the superiority of Structure/75.html">Prediction Methods Based on specific sequence information demonstrates that IDP sequences contain additional information regarding structural disorder. The number of sequences with experimentally verified disordered structures is small, which limits the investigation of their higher-order properties. Nevertheless, this issue has already been addressed in several studies. By describing Amino Acids in terms of Hydrophobicity, polarity, size, aliphatic/aromatic nature, the presence of a heterocyclic component (Proline), and charge, simple yet statistically significant sequence patterns can be identified through the analysis of disordered segments (Lise and Jones 2005). Research has demonstrated the prevalence of proline-rich patterns, as well as charged patterns arising from the presence of positively or negatively charged amino acids (e.g., Positive aa)-Pos-Pos, Negative aa)-Neg-Neg, as well as Glu-Glu-Glu, Lys-X-X-Lys-X-Lys, and Pro-X-Pro-X-Pro). Thus, local Sequence Motifs are associated with protein disorder; this fact can be explained by the Abundance of repeats, which is widely recognized as one of the evolutionary mechanisms of IDPs—a process that evidently gives rise to such repetitive motifs within sequences (Tompa 2003).