The evolution of human metalloproteinases shows that addition of new domains at different stages of evolution extends the functionality of proteins while preserving their core functionality.
According to the neutral theory of evolution, the functionality of protein with disadvantageous amino acid substitution can be restored by another amino acid substitution which compensates the first one to sustain the fitness [1].
The incorporation of a dual function in one molecule will not provide the necessary flexibility for the individual evolution of the different functionalities.
In summary, primitive type-3 copper proteins, probably tyrosinases, are likely to have exhibited broad activities and/or substrate affinities, and subsequent fine-tuning of the active site enabled the evolution of the different functionalities of catechol oxidases, tyrosinases, tyrosinase related-proteins and hemocyanins in extant animals.
Standard thinking says that the evolution of complex functionality proceeds by the addition of new parts, and that this build-up of complexity is driven by selection, by the functional advantages of complex design.
As such, neofunctionalization may itself lead to a situation where gene family expansion is selectively favorable, an observation that complements the general model where gene duplication predates and facilitates the evolution of novel functionality.
This result was expected, since the evolution of the system includes new functionalities and God Classes tends to centralize them.
3,4-DHPEA-EA (methyl-4- 2- 3,4-dihydroxyphenethoxy -2-oxoethyl -3-formyl-2-methyl-3,4-dihydro-2H-pyran-5-carboxylate) methyl-4- 2- 3,4-dihydroxyphenethoxy -2-oxoethyl -3-formyl-2-methyl-3,4-dihydro-2H-pyran-5-carboxylateetal methyl-4- 2- 3,4-dihydroxyphenethoxy -2-oxoethyl -3-formyl-2-methyl-3,4-dihydro-2H-pyran-5-carboxylate
These studies support the hypothesis that retrogenes played an important role in the evolution of functionality in organisms.
The phylogenetic hypotheses presented here may be used to understand the evolution of GH20 family functionality in eukaryotes.
