Physical and Evolutionary Free Energy Landscapes of Devolved Protein Sequences

Protein evolution is guided by structural, functional, and dynamical constraints ensuring biological viability. Pseudogenes are former protein-coding genes identified in numerous prokaryotic and eukaryotic organisms that lack translational activity due to sequence deterioration. The resulting loss of selection pressure makes pseudogenes an intriguing example of naturally-occurring protein devolution. Mutational effects on pseudogenes’ former native structure and function remain largely unexplored in the literature. We characterized the physical and evolutionary free energy landscapes of human pseudogenes associated with various protein domains, respectively using the optimized physical model Associative Memory, Water Mediated, Structure and Energy Model (AWSEM) and the coevolutionary model Direct Coupling Analysis (DCA). We found that pseudogene mutations disrupt their native global network of stabilizing residue interactions. We also investigated pseudogene sequence variations in Cyclophilin A, Profilin-1, and SUMO-2 Protein that are more energetically favorable than native residues. Our analysis reveals that physically stabilizing mutations inhibit or alter pseudogenes' former biological activity.