The evolution of multiple active site configurations in a designed enzyme

Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis

Duplication and divergence of the Psb27 subunit of Photosystem II in the green algal lineage

<div><p>Photosystem II (PSII) is subject to light-induced damage and continuously undergoes repair to restore the damaged photosystems. During repair of PSII, the Psb27 protein interacts with the CP43 subunit of PSII. Two Psb27-like proteins (Psb27-H1 and Psb27-H2) are involved in the repair of PSII in the higher plant <i>Arabidopsis thaliana</i>. Here, we present evidence that duplication and divergence of Psb27 occurred in the green algal lineage and that the Psb27-H2 protein shares c. 30% sequence identity with Psb27-H1. Structural modelling of <i>Arabidopsis thaliana</i> Psb27-H1 and Psb27-H2 indicate that the two proteins have different distributions of surface charge. We suggest that the green algal lineage Psb27-H2 protein occupies a different binding niche than does Psb27-H1.</p></div