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

Bioinformatics Methods for Studying the Structure and Function of Disordered Proteins
Limitations of IDP Function Prediction Methods
Rapid Evolution of IDPs

As already clear from the previous sections, predicting IDP/IDR Functions from sequence alone remains fraught with ambiguity. The complexities involved can be addressed in various ways that are nonetheless closely intertwined, resting fundamentally on the rapid evolution of IDPs and the decoupling of sequence from function. These aspects will be discussed in greater detail in the final section.

The rapid evolution of IDPs/IDRs has been directly demonstrated by comparing amino acid substitution rates in disordered and globular regions within Protein Families that contain both types of domains (Brown et al. 2002). For 26 such families, a statistical measure of Variability (mean genetic distance) was calculated by comparing every pair of sequences in multiple alignments. The results showed that in 19 families, disordered regions evolve much faster than ordered ones; in 5 families, the evolutionary rates are nearly identical; and in only 2 families are the evolutionary rates for disordered regions noticeably lower than for ordered ones. Regarding function, no simple rules can be established, since rapidly evolving regions include protein-, DNA-, and RNA-binding sites, and can also act as flexible linkers. For slowly evolving disordered regions, the picture is clearer: most of them are involved in DNA binding and also form extensive interaction interfaces with partner molecules. These interaction sites likely serve as a constraint that limits acceptable sequence variations (Brown et al. 2002).

This issue has been addressed in two studies. Holt and Sawyer compared substitution rates in the translated and untranslated Regions of the casein Gene (Holt and Sawyer 1988). They found that the region encoding the Amino Acid Sequence evolves faster—meaning it apparently experiences fewer evolutionary constraints—than the untranslated region responsible for Translation regulation. In another study, Dodrill and colleagues (2007) analyzed the evolution and function of the disordered linker region connecting two globular domains in the 70 kDa subunit A of the Replication protein RPA70 (Olson et al. 2005). An analysis of evolutionary rates revealed that the linker region is highly variable, with many segments evolving at an intermediate rate. Linker flexibility was investigated using NMR spectroscopy. Direct measurements of backbone flexibility, such as residual dipolar couplings and rotational correlation times, demonstrated that the backbone flexibility profile is conserved despite substantial sequence variability. These findings emphasize that pronounced sequence variability is compatible with the preservation of function, which in turn greatly complicates attempts at functional prediction.