Mechanistic Insights of β-Lactmases Evolution

β-lactmases, the enzymes produced by some bacteria, are responsible for the primary mechanism of resistance to β-lactam antibiotics, the most common antibiotics in commercial use. Earlier study has resurrected a series of ancient Class A β-lactmases in the laboratory. It showed that those 2-3 Gyr-old β-lactmases could degrade a variety of antibiotics in vitro with similar levels of catalytic efficiency, suggesting that β-lactmases evolve from substrate-promiscuous generalists to specialists. However, all those ancient β-lactmases adopt the same fold as the modern enzyme, especially at the catalytic sites. Here we propose that the enhanced substrate-promiscuity originates from protein dynamics. We investigate the differences in conformational dynamics of diverged β-lactmases through MD simulation and quantify the contribution of each residue site to functionally related dynamics through Dynamic Flexibility Index (DFI). The statistical clustering of the DFI pattern is later obtained through Principle Component Analysis (PCA). Strikingly, our result shows that those 2-3 Gyr-old β-lactmases are clustered together and far away from the modern enzyme in the principle subspace. This dynamic analysis also identifies those sites affecting dynamics the most that may play a critical in functional evolution of β-lactmases.