When to make proteins - and which ones - is a critical decision for a cell, and one which must be constantly under revision as circumstances change. One protein, eIF2a, is a central regulator of protein synthesis. As eIF2a is an essential part of the machinery which synthesises proteins it makes a good 'checkpoint'. Of course the 'machinery' aka ribosomes, are vastly complex and amazing entities and there are plenty of other regulatory and checkpoint mechanisms - but for now we'll just look at eIF2a.
The activity of eIF2a is controlled is by phosphorylation; the reversible addition of a little phosphate group by a kinase (which is a protein too). So phosphorylation acts like a on/off switch. A kinase called PKR can add phosphate to eIF2a and halt protein synthesis. Here's what these two proteins look like in a cartoon format:
PKR is shown in green on the right hand side and eIF2a in blue on the left. Note the little point of contact between the two a helix sticking out of PKR and the barrel of sheets in eIF2a. The crucial phosphrylation, by the way, is on one of those two strands which cross over the barrel. This imlies that PKR must coil around eIF2alpha to reach there.
PKR helps to defend a cell from viral attack, it is activated by the double stranded RNA found in several types of virus, and then rushes off to phosphorylate eIF2a and shut down protein synthesis. This works brilliantly as a defence because many viruses are nothing more than a bit of genetic material (DNA or RNA) coated with protein. Well, it did work brilliantly until some canny viruses - the pox amongst them - evolved proteins which mimic eIF2a and shut down PKR by binding tightly to the defender. If PKR is out of action then the cell can no longer shut down protein synthesis and thus avoid being hijacked by the virus. The pox virus has such a mimic protin called K3L and, as you can see below, K3L looks quite like eIF2a. The virus protein has only got that little barrel and a bit of a neighboring helix but it is enough to do the job of binding to PKR.
Well Elde and co. figured that PKR has a problem; it must be able to recognise its correct target, eIF2a, but would like to avoid binding to pesky viral mimics such as K3L. The structure of eIF2a can't change easily because it has such an important role in a complex machine - initiating protein synthesis in the ribosome - and therefore must fit snugly like a jigsaw piece. In fact eIF2a is one of the most highly conserved proteins, for example, the amino acid sequence of eIF2a of yeast and humans are astonishingly alike. So the virus in wants to copy eIF2a to fool PKR. Such an interaction is often described as an arms race. Sometimes K3L binds to PKR and the virus 'wins' and smallpox rages across countries, wiping out everyone with PKR proteins that fail to spot the intruder. Many of the survivors will, by necessity, have a variant form of PKR which can discriminate between the correct eIF2 and the dangerous decoy. To survive in the population the virus has to re-adapt the mimic protein. In midst of a smallpox epidemic having the 'right' form of PKR is a big advantage and this is a fundamental bit of evolution, the virus is applying a selection pressure on PKR. It's adapt or die.
If we look over evolutionary time we should be able to figure out which parts of PKR are responsible for recognising the mimics. How can we do this? Well, all proteins change slowly over the generations due to little errors made when copying DNA. For many parts of a protein this change may not be very important; it can still do its job well enough. If the mutation hits an important part though, such as eIF2 binding to a ribosome, well then that unfortunate individual will die (or fail to reproduce; this is the same to evolution) and the mutation will be lost. The important part of the protein - critical amino acids - will remain more unchanged than one would expect by chance alone and such parts of the protein are said to be under 'positive selection pressure'. If an external agent - such as a virus - applies the pressure then, somewhat tactlessly, biologists call this 'purifying selection'.
To find out if such selection occurs and which parts of PKR might be important in the eIF2a vs. K3L story Elde looked at DNA sequences of PKR from 20 primate species which cover about 30 million years. (Don't worry it's very unlikely any primates were killed for this work, a small tissue sample would be more than enough. In fact the information is probably already sitting in genbank .) They found that amino acid residue which line the interface between PKR and eIF2a have been subject to intense episodes of positive selection. In other words PKR in our bodies today still bears the marks from devastating epidemics thousands - or hundreds of thousands - or years ago when ALL variant forms of PKR were wiped out, along with their unlucky host. I find it astonishing that a disease - a little virus - can shape our proteins, indeed shape our evolution. I got kind of dizzy thinking about waves of epidemics and so much death - and yet here we are with hundreds of thousands of proteins making up our bodies, all shaped by various forces, many carrying remains of past evolutionary battles but still we rattle along.
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