We’ve been talking about protein structure and folding in my Biol 105 class. Proteins are made of chains of amino acids and the sequence of amino acids, or primary structure, dictates the way the protein will fold into its final 3D or tertiary structure. We may assume that two proteins with similar sequences would have a similar structure, and that two proteins with very different sequences would have different structures. However, this is not true. Proteins with very different sequences can end up with similar 3D structures.
A great example of this is the structure of capsid proteins from three very different viruses. Adenoviruses infect animals (eukaryotes), and is one of many viruses that cause colds. PRD1 is a bacteriphage, a virus that infects bacteria. STIV (Sulfolobus turreted icosahedral virus) infects Sulfolobus, an archaea that lives in geothermal hotsprings in Yellowstone National Park. STIV and its host love the 80 degree celsius, pH 3 environment of the hotsprings. The fact that there are viruses that infect archaea in those extreme environments is cool enough. But it turns out that the capsid proteins of these three viruses are actually quite similar. Their sequence differs significantly, but their tertiary structures are highly similar, meaning these very different polypeptides fold into essentially the same shape.
What is the basis of this similarity? Do all theses viruses share a common ancestor, which would have existed before the three domains of cellular life (eukarya, bacteria, archaea) diverged over 3 billion years ago? Is it convergent evolution? Was there a horizontal gene transfer event in which a gene moved among all three domains? The authors of the paper argue for a common ancestor but the other possibilities have not been formally excluded. We still don’t really know, and it raises interesting questions about the origin of viruses.
I agree that the similarities in virus structure is most likely due to convergent evolution rather than similar ancestry. Acknowledging the fact that each virus inhabits seemingly drastically different hosts and environments, it cannot be assumed that differing environments always call for differing structures. For example, a knife can work well for cutting a slice of bread, and can also work well as an alternative to a screw-driver. These viruses are a good example of how identical structure can warrant varying functions.
Responding to the above question, I would argue that, being one effective conformation of the capsid protein, it’s not an unlikely scenario to be arrived at by more than one evolutionary pathway. I feel that arrangement of amino acids would be the only real effective measure of biological ancestry on the molecular level, as reaching the same capsid conformation with very different amino acid combinations, under my understanding, would potentially entail hundreds of millions of years’ worth of single amino acid changes if reached on the same evolutionary pathway. The amount of potential ways to construct a self-assembling capsid protein seems relatively limited enough in scope to give coincidental structural similarities a greater probability than such evolutionary connections.
Saumya and Alex both argue for convergent evolution. Saumya is right that interactions between side-chains (and backbone actually) determine the overall structure and that there is more than one way to skin a cat, so to speak, so to me its also not that surprising that different sequences could result in similar structures. But what about the fact that there are several different virus morphologies that are observed in viruses infecting each of the domains. That is, you dont need this exact structure to infect. Helical and other shapes of viruses exist and they exist in viruses infecting all domains of cellular life. So if you dont need this exact shape, why would it evolve independently?
There are many factors that influence host range, or the ability to infect different hosts. The molecular and cellular components of each of these hosts are extraordinarily different from eachother, and usually viruses are limited to closely related hosts. So in this case, the similar structures of these capsid proteins does not confer a broad host range. It would be interesting to determine if there are structural similarities in the host receptors however, since one might expect that a similar capsid structure would bind a similar receptor structure.
I think that in this case, the similarities between capsid proteins is an example of convergent evolution. Archaea have fundamentally different membranes and cellular processes. This, and the inhospitable environment of Sulfolobus is inhospitable are likely to have funneled potential pathogens into a particular mechanism of infection. I think that common ancestry is unlikely, given that at the molecular level most homologous structures share some similarities, unlike the three viruses.
Speculation: The similarities of the tertiary structures come from the interactions between the R groups, correct? Thus I feel as though because there are so many R groups in each of the polar, non-polar, basic, acidic, etc categories that it isn’t that surprising that such structures would be similar. I don’t think that this necessarily means that there is a common ancestor because although the 3d shapes are similar, that doesn’t really warrant that the sequence is similar. Just some thoughts of mine. There is a very good chance I could be totally off.
Question: If a virus, bacteriophage or any other virus (e.g. STIV – as mentioned in the post) have very similar structures, does this mean that each respective virus has the potential to or can infect the others host? That is, for example, since adenoviruses and PRD1 are similar, can adenoviruses infect certain types of bacteria or can PRD1 infect certain types of eukaryotes?