Intrinsically disordered regions of proteins are frequent in nature, and they have important functions in the interior of cells. As we have already seen, proteins often have loops of polypeptide chain that protrude from the core region of a protein domain to bind other molecules. Some of these loops remain largely unstructured until they bind to a target molecule, adopting a specific folded conformation only when this other molecule is bound. Many proteins were also known to have intrinsically disordered tails at one or the other end of a structured domain (see, for example, the histones in Figure 4–24). But the extent of such disordered structure only became clear when genomes were sequenced. This allowed bioinformatic methods to be used to analyze the amino acid sequences that genes encode, searching for disordered regions based on their unusually low hydrophobicity and relatively high net charge. Combining these results with other data, it is now thought that perhaps a quarter of all eukaryotic proteins can adopt structures that are mostly disordered, fluctuating rapidly between many different conformations. Many such intrinsically disordered regions contain repeated sequences of amino acids. What do these disordered regions do?
Some known functions are illustrated in Figure 3–24. One predominant function is to form specific binding sites for other protein molecules that are of high specificity, but readily altered by protein phosphorylation, protein dephosphorylation, or any of the other covalent modifications that are triggered by cell signaling events (Figure 3–24A and B). We shall see, for example, that the eukaryotic RNA polymerase enzyme that produces mRNAs contains a long, unstructured C-terminal tail that is covalently modified as its RNA synthesis proceeds, thereby attracting specific other proteins to the transcription complex at different times (see Figure 6–22). And this unstructured tail interacts with a different type of low complexity domain when the RNA polymerase is recruited to the specific sites on the DNA where it begins synthesis.
As illustrated in Figure 3–24C, an unstructured region can also serve as a “tether” to hold two protein domains in close proximity to facilitate their interaction. For example, it is this tethering function that allows substrates to move between active sites in large multienzyme complexes (see Figure 3–54). A similar tethering function allows large scaffold proteins with multiple protein-binding sites to concentrate sets of interacting proteins, both increasing reaction rates and confining their reaction to a particular site in a cell (see Figure 3–78).
Like elastin, other proteins have a function that directly requires that they remain largely unstructured. Thus, large numbers of disordered protein chains in close proximity can create micro-regions of gel-like consistency inside the cell that restrict diffusion. For example, the abundant nucleoporins that coat the inner surface of the nuclear pore complex form a random coil meshwork (Figure 3–24) that is critical for selective nuclear transport (see Figure 12–8).
Figure 3–24 Some important functions for intrinsically disordered protein sequences. (A) Unstructured regions of polypeptide chain often form binding sites for other proteins. Although these binding events are of high specificity, they are often of low affinity due to the free-energy cost of folding the normally unfolded partner (and they are thus readily reversible). (B) Unstructured regions can be easily modified covalently to change their binding preferences, and they are therefore frequently involved in cell signaling processes. In this schematic, multiple sites of protein phosphorylation are indicated.
(C) Unstructured regions frequently create “tethers” that hold interacting protein domains in close proximity. (D) A dense network of unstructured proteins can form a diffusion barrier, as the nucleoporins do for the nuclear pore.