Hello Manas,

Yes.. the scenario that you have presented is convergent i.e. different proteins sharing same function. But if we look at the bigger picture, many similar kind of structures are evolving themselves for different functions as the nature and evolution demands.. so it'll be difficult to assign convergent or divergent way to protein structure evolution, as both things happen in nature. But according to me, more generally it'll be divergent as they have to cope up with increasing number of diverse conditions and develop new functions to adapt to new environmental conditions.

one of the example could be of chironomous hemoglobin. We know that the hemoglobin is oxygen transporter molecule. But in chironomous, it has to live in hypoxic conditions so its hemoglobin structure has evolved to store oxygen as well like myoglobin in our case so that it can live in hypoxic conditions also. There are several examples like this.

This is actually a tricky question due to your “or” statement – “non-homologous or functionally unrelated proteins tend to share the same domain.” Homologous structures have a common origin, but not necessarily a similar function. So functionally unrelated proteins with the same structure might well be divergent. Non-homologous proteins that share a structure would be by definition convergent. But then one might expect that the convergence was driven by some shared function. Domains arising via convergent evolution can be called analogous rather than homologous structures. However, functionally unrelated proteins might be convergent if the convergence was driven by achieving an especially favorable fold for general classes of functions, such as binding partners or co-factors or signaling. Likely in the long sense many protein folds are divergent from ancestor domains that happened to allow multiple sequences to fold into stable units of three-dimensional structure. We know that there are a limited number of folds compared to the number of different protein sequences and this realization drove the original Protein Structure Initiative (PSI) to determine exemplary structures for all folds so that structurally homologous or analogous proteins might be computationally modeled whether convergent or divergent (see http://www.nigms.nih.gov/news/reports/protein_structure.htm). This idea was largely abandoned in subsequent rounds of PSI projects (see http://www.nigms.nih.gov/Research/FeaturedPrograms/PSI/psi_biology/). Anyway in general the domains you are considering may be either divergent or convergent, if you are assuming they are not homologous simply by sequence identify.

Thanks for the answer. About the proteins being non homologous is based predominantly on their sequence identity. at the same time their functions appear to be different as well. The concept of the domains being analogous seems an interesting concept. But can that be proved? furthermore, how can or is it possible to prove whether a domain is a result of convergent or divergent evolution?

It is hard to prove convergent or divergent evolution, but you can certainly infer things to support one of the other. For example, the ABC ATPase superfamily has membrane and DNA repair components but conserved signature sequence and Arg helix – these different membrane and DNA repair members have likely diverged from a common ABC ATPase progenitor even though you may not see statistically significant sequence identity overall. When functional residues are positioned on sequence unrelated frameworks but spatially arranged in an analogous way, then this is usually believed to be the result of convergent evolution. So analogy can be supported by structural comparison and identification of functional similarities done in different ways such as the development of an electrostatic loop on another but comparable region to achieve a similar function.

very clear, John. Thanks!