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The ability to create efficient artificial enzymes for any chemical reaction is of great interest. Here, we describe a computational design method for increasing the catalytic efficiency of de novo enzymes by several orders of magnitude without relying on directed evolution and high-throughput screening. Using structural ensembles generated from dynamics-based refinement against X-ray diffraction data collected from crystals of Kemp eliminases HG3 ( k cat / K M 125 M -1 s -1 ) and KE70 ( k cat / K M 57 M -1 s -1 ), we design from each enzyme ≤10 sequences predicted to catalyze this reaction more efficiently. The most active designs display k cat / K M values improved by 100-250-fold, comparable to mutants obtained after screening thousands of variants in multiple rounds of directed evolution. Crystal structures show excellent agreement with computational models, with catalytic contacts present as designed and transition-state root-mean-square deviations of ≤0.65 Å. Our work shows how ensemble-based design can generate efficient artificial enzymes by exploiting the true conformational ensemble to design improved active sites.

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (k cat /K M 146 M -1 s -1 ). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (k cat /K M 103,000 M -1 s -1 ) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

We report synchrotron X-ray diffraction, photoconductivity, and photoluminescence investigations of methylammonium-lead-bromide (MAPbBr 3 ) under various stress conditions, supported by density-functional-theory (DFT) calculations. The properties of MAPbBr 3 show substantial dependence on the hydrostatic conditions. While nonhydrostatic compression of MAPbBr 3 leads to amorphization above 2.4 GPa, under quasi-hydrostatic (Ar) and hydrostatic (He) pressure, the sample remains in crystalline phases. A sequence of phase transitions between two cubic phases and orthorhombic Pnma phase is observed when using Ar, or no pressure-transmitting-medium (PTM). In helium-PTM only transitions between the two cubic structures and a new isostructural phase transition with a large volume collapse to a third cubic-phase at 2.7 GPa was observed. The photoluminescence measurements indicate a pressure-induced band gap-narrowing in the cubic phase I, and a blue-shift in the orthorhombic structure. DFT calculations illustrate that the dynamics of the organic molecules and the inorganic lattice, coupled via the N-H···Br hydrogen-bonding interactions, affect the Pb-Br distance and the bandgap evolution under pressure.

First principles structural prediction and molecular dynamics (MD) calculations have been performed to examine the structures responsible for the recently reported metallic and superconducting phases of highly compressed CS2. The low pressure experimental molecular crystal structure was found to be metastable and transformed into a disordered structure above 10 GPa. At 60 GPa, the predicted low energy structures show molecular CS2 is separated into C and S dominant regions. A crystalline structure with the P21/m symmetry was found to be most stable from 60 to 120 GPa. The structure is formed from alternate layers of hexagonal C rings and S 2D-square-nets linked by C-S bonds. A non-crystalline structure with similar features structure is also predicted by MD calculations. Electron-phonon coupling calculations show this crystalline phase is superconductive. Contrary to the suggestions made from the experiments, no magnetism was found in all predicted low enthalpy high pressure structures. Moreover, the theoretical results do not support the proposal on the existence of hypervalent 6-coordinated carbon at 120 GPa.