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

Bioinformatics Methods for Studying the Structure and Function of Disordered Proteins
Limitations of IDP Function Prediction Methods
Conservation and Disorder

As a final remark, it should be noted that disorder is not strictly the opposite of sequence conservation, as some disordered regions are evolutionarily conserved (Chen et al. 2006a, b). A comprehensive study of domain families conducted by Dunker and colleagues showed that many Regions of the studied Proteins, containing at least 20 amino acid residues, are characterized by significant conservation. Such regions were termed conserved disorder predictions (CDPs) and were found in nearly 30% of domain families. Most CDPs are short, with only 9% containing more than 30 residues; typically, they cover less than 15% of the corresponding domain. The longest CDP, however, contains 171 amino acid residues (in the dentin matrix protein). Perhaps even more importantly, 8.7% of CDPs cover more than half of their corresponding domains, and 16 CDPs cover the entire domain. The Functions of domains containing CDPs correspond to the general functional features of IDPs, such as DNA/RNA binding, ribosome Structure formation, and protein binding (both signaling functions/regulation and complex formation). Although these data are not yet used in function prediction, they may serve as a basis for important Applications in the future.