From Protein Structure to Function with Bioinformatics.pdf

5 Structure and Function of Intrinsically Disordered Proteins 133families. In a functional sense, no simple rules could be established, as the fasterevolvingdisordered regions include binding sites for proteins, DNA, and RNA, andmay also serve as flexible linkers. The situation of more slowly evolving disorderedregions is clearer, most of them being involved in DNA binding and engaging inextensive contacts with the partner. These contacts have probably limited acceptablechanges in the sequence (Brown et al. 2002).This issue was directly addressed in two other studies. Holt and Sawyer comparedthe replacement rate of the translated and non-translated regions of the geneof casein (Holt and Sawyer 1988). It was found that the region that actually encodesfor the amino acid sequence evolves faster, i.e. it is apparently subject to fewerevolutionary constraints than the non-translated region involved in interactions regulatingtranslation. In another study, Daughdrill and colleagues (2007) analyzed theevolution and function of the disordered linker region connecting two globulardomains in the 70 kDa subunit of replication protein A, RPA70 (Olson et al. 2005).Evolutionary rate studies showed large variability within the linker, with many sitesevolving neutrally. Flexibility of the linker was studied by NMR spectroscopy.Direct measures of backbone flexibility, such as residual dipolar coupling and thetime of Brownian reorientation showed that the pattern of backbone flexibility isconserved despite large sequence variations. These results underscore that largesequence variation is compatible with preservation of function, a finding which ishighly detrimental to function prediction efforts.5.6.2 Sequence Independence of Function and FuzzinessIn keeping with these points, several recent mutagenesis studies have pointed to aunconventional relationship between sequence and function in IDPs. In these studies,sequences of functional regions were scrambled, but function was found to berather insensitive to randomization. The phenomenon is usually termed sequenceindependence (Ross et al. 2005; Tompa and Fuxreiter 2008). These observationsunderscore the limitations in our understanding of the relationship of sequence andfunction in IDPs.The classical observation comes from transcription factors, where the acidictrans-activator domain (TAD) of Gcn4p could be replaced with random acidicsegments without a major loss of biological activity (Hope et al. 1988). The possiblegenerality of this behaviour has led to the suggestion that the assembly ofthe transcriptional pre-initiation complex may not require the usual strict geometriccomplementarity demanded by specific protein-protein recognition(Sigler 1988). In a detailed follow-up study with the chimeric transcription factorEWS fusion protein (EFP), a similar behaviour was observed (Ng et al. 2007).In the highly repetitive TAD of EFP, individual repeats could be freely interchanged,their sequences randomized or even reversed, without the loss of EFPfunction.