It has recently been shown that many proteins are unfolded in their functional state. In addition, a large number of stretches of protein sequences are predicted to be unfolded. It has been argued that the high frequency of occurrence of these predicted unfolded sequences indicates that the majority of these sequences must also be functional. These sequences tend to be of low complexity. It is well established that certain types of low-complexity sequences are genetically unstable, and are prone to expand in the genome. It is possible, therefore, that in addition to these well-characterised functional unfolded proteins, there are a large number of unfolded proteins that are non-functional. Analogous to ‘junk DNA’ these protein sequences may arise due to physical characteristics of DNA. Their high frequency may reflect, therefore, the high probability of expansion in the genome. Such ‘junk proteins’ would not be advantageous, and may be mildly deleterious to the cell.
Fast forward to 2013:
In 2013 functions were identified for many of these “intrinsically disordered proteins” (IDPs), as they are sometimes called. Functions such as crucial roles in regulating ion channels and molecular hubs in intracellular signaling networks. A friend points us to:
 Bozoky Z, Krzeminski M, Chong PA, Forman-Kay JD (2013) Structural changes of CFTR R region upon phosphorylation: A plastic platform for intramolecular and intermolecular interactions. FEBS J 280:4407-4416. doi:10.1111/febs.12422
 Ferreon ACM, Ferreon JC, Wright PE, Deniz AA (2013) Modulation of allostery by protein intrinsic disorder. Nature 498:390-394. doi:10.1038/nature12294
 Cumberworth A, Lamour G, Babu MM, Gsponer J (2013) Promiscuity as a functional trait: Intrinsically disordered regions as central players of interactomes. Biochem J 454:361-369. doi:10.1042/BJ20130545
See also: The Myth of Junk DNA.
If you came late, you missed all the fun around “It is so just junk!”
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