The Impact of Native State Switching on Protein Sequence Evolution

For proteins with a single well-defined native state, protein 3Dstructure is a major determinant of sequence evolution. On the other hand, many proteins adopt multiple, distinct native structures under different conditions ("conformational switches"), yet the impact of such native state switching on protein evolution is not fully understood. Here, we performed a proteome-wide analysis of how protein structure impacts sequence evolution for protein conformational switches in Saccharomyces cerevisiae using pooled analysis of sites with similar packing or burial. We observed a strong linear relationship between residue evolutionary rate and residue burial for conformational switches. In addition, we found that conformational switches evolve significantly and consistently more slowly than proteins with a single native state, even after controlling for degree of residue burial or packing. Next, we focused on proteins that switch conformations upon molecular binding. We found that interfacial residues in these conformational switches evolve more slowly than interfacial residues in proteins with a single native state, and that the bound conformation is a better predictor for residue evolutionary rate than the unbound conformation. Our findings suggest that for conformational switches, the necessity to encode multiple distinct native structures under different conditions imposes strong evolutionary constraints on the entire protein, rather than just a few key residues. Our results provide new insights into the structure-evolution relationship of protein conformational switches.