Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4.

Producing novel enzymes that are catalytically active in vitro and biologically functional in vivo is a key goal of synthetic biology. Previously, we reported Syn-F4, the first de novo protein that meets both criteria. Syn-F4 hydrolyzed the siderophore ferric enterobactin, and expression of Syn-F4 allowed an inviable strain of Escherichia coli (Δfes) to grow in iron-limited medium. Here, we describe the crystal structure of Syn-F4. Syn-F4 forms a dimeric 4-helix bundle. Each monomer comprises two long α-helices, and the loops of the Syn-F4 dimer are on the same end of the bundle (syn topology). Interestingly, there is a penetrated hole in the central region of the Syn-F4 structure. Extensive mutagenesis experiments in a previous study showed that five residues (Glu26, His74, Arg77, Lys78, and Arg85) were essential for enzymatic activity in vivo. All these residues are located around the hole in the central region of the Syn-F4 structure, suggesting a putative active site with a catalytic dyad (Glu26-His74). The complete inactivity of purified proteins with mutations at the five residues supports the putative active site and reaction mechanism. Molecular dynamics and docking simulations of the ferric enterobactin siderophore binding to the Syn-F4 structure demonstrate the dynamic property of the putative active site. The structure and active site of Syn-F4 are completely different from native enterobactin esterase enzymes, thereby demonstrating that proteins designed de novo can provide life-sustaining catalytic activities using structures and mechanisms dramatically different from those that arose in nature.

Superalkali-Alkalide Interactions and Ion Pairing in Low-Polarity Solvents.

The nature of anionic alkali metals in solution is traditionally thought to be "gaslike" and unperturbed. In contrast to this noninteracting picture, we present experimental and computational data herein that support ion pairing in alkalide solutions. Concentration dependent ionic conductivity, dielectric spectroscopy, and neutron scattering results are consistent with the presence of superalkali-alkalide ion pairs in solution, whose stability and properties have been further investigated by DFT calculations. Our temperature dependent alkali metal NMR measurements reveal that the dynamics of the alkalide species is both reversible and thermally activated suggesting a complicated exchange process for the ion paired species. The results of this study go beyond a picture of alkalides being a "gaslike" anion in solution and highlight the significance of the interaction of the alkalide with its complex countercation (superalkali).