An interesting feature of many proteins is a disordered region down at the carboxy end. The reason for this feature has been obscure: if there’s part of the protein that just spends its days flailing around uselessly, why go to the trouble of translating it? Many of these tails certainly seem to have no defined structural role, because you can mutate their sequences in all sorts of ways with no apparent problems. How have such things persisted in the absence of any obvious function? The answer, as is so often the case in biology, is that there’s function but it’s not too obvious.
Here’s a paper looking at an enzyme called UDP-α-D-glucose-6-dehydrogenase (UGDH) that has such a disordered 30-amino acid tail. You can chop the whole thing off and the enzyme has what seem to be basically the same kinetics, so what’s it doing there? As it turns out, you have to look closer. The enzyme is allosterically regulated by UDP-α-D-xylose, a negative feedback system. It’s an unusual one, because the same active site serves both purposes – the enzyme forms an inactive hexamer that can break up into three active dimers, and this switch is dependent on competition between the UDP-α-D-glucose substrate and the UDP-α-D-xylose allosteric ligand.
And it’s true that the substrate behavior doesn’t seem to change in the absence of the disordered tail. But the allosteric behavior sure does: without those thirty residues, the affinity for the xylose ligand is tenfold lower. The group tried a whole range of mutations in that region to see if any affected this behavior, but it was pretty impervious: swapping out all the prolines, no effect. Switching all the lysines to serines: no effect. Turning the whole darn thing to nothing but thirty serines in a row: no effect. Varying the length of that chain showed a simple exponential-decay relationship with the UDP-α-D-xylose affinity: the longer the better, out to around thirty or so. But even a four-serine tail has an effect.
What the disordered tail is doing here, regardless of sequence, seems to be tied to entropic effects. The authors note that if you hang an unstructured polymer off a surface, you generate an entropic effect down at the point of attachment. That’s because the surface itself excludes some conformations of the polymer, and thus reduces entropy. Hydrogen-deuterium exchange experiments (a method that shows how exposed and mobile a protein’s regions are) shows that the tail region completely exchanges within about two minutes, and that its presence alters the exchange rates of several other parts of the UGDH protein, especially around the binding site. The entropic cost of constraining that disordered tail, in other words, energetically biases the protein towards conformations that are more favorable for binding the allosteric regulator. Doesn’t matter what the tail consists of, so long as its disordered and about that length.
That’s interesting enough by itself (well, to me anyway – I admit that mileage may vary on a topic like this one!) What’s odd is that the tail region is nonetheless highly conserved. This in the face of compelling evidence that its sequence doesn’t matter for this function! The best explanation is that it may have still other (unknown) biological functions that require a particular structure/sequence; it’s just this one isn’t one of them. Which means that in some ways it’s important that this region be disordered, any old way, and in other ways it’s important that it has a particular sequence and presumably particular interactions. That’s what three billion years of whatever-works-dude tinkering will get you. As an unavoidably snarky aside, if anyone can provide an analogy to this behavior to what’s seen in coding, hardware design, or any sort of human engineering at all, please speak up.