Dimer-assisted mechanism of (un)saturated fatty acid decarboxylation for alkene production

Coordinated conformational changes in P450 decarboxylases enable hydrocarbons production from renewable feedstocks

Fatty acid peroxygenases have emerged as promising biocatalysts for hydrocarbon biosynthesis due to their ability to perform C-C scission, producing olefins - key building blocks for sustainable materials and fuels. These enzymes operate through non-canonical and complex mechanisms that yield a bifurcated chemoselectivity between hydroxylation and decarboxylation. In this study, we elucidate structural features in P450 decarboxylases that enable the catalysis of unsaturated substrates, expanding the mechanistic pathways for decarboxylation reaction. Combining X-ray crystallography, molecular dynamics simulations, and machine learning, we have identified intricate molecular rearrangements within the active site that enable the Cβ atom of the substrate to approach the heme iron, thereby promoting oleate decarboxylation. Furthermore, we demonstrate that the absence of the aromatic residue in the Phe-His-Arg triad preserves chemoselectivity for alkenes, providing a distinct perspective on the molecular determinants of decarboxylation activity. Ultimately, these findings enable the sustainable production of biohydrocarbons from industrial feedstocks.

Surface Defect-Induced Specific Catalysis Activates 100% Selective Sensing toward Amine Gases at Room Temperature

Achieving selective sensing toward target volatile organic compound gases is of vital importance in the fields of air quality assessment, food freshness evaluation, and diagnosis of patients via exhaled breath. However, chemiresistive sensors that exhibit specificity like biological enzymes in a complex environment are rare. Herein, we developed a strategy of optimizing oxygen vacancy structures in tin oxides to induce specific catalysis, activating 100% selective sensing toward amine gases at room temperature. In situ technologies and theoretical calculations reveal that the "donor-receptor" coordination between nitrogen atoms from amine molecules and bridging oxygen vacancies (OVBri)-induced electron-deficient center is the essence of specific catalysis and provides the bridge from the surface oxidation reaction to electrophysical characteristics evolution, which allows the sensor to exhibit amine-specific sensing behavior, even in gas mixtures. Moreover, OVBri enhances the selectivity by enabling a room-temperature sensing pathway where lattice oxygens participate in catalytic oxidation for amine molecules, resulting in record-high sensing values: 19,938.92 toward 100 ppm of triethylamine, 15,236.78 toward trimethylamine, and 123.41 toward diethylamine. Our findings illustrate the feasibility of designing specific active sites through defect engineering and can contribute to the advancement of highly selective sensors based on catalytic processes.

Decarboxylation in Natural Products Biosynthesis

Decarboxylation reactions are frequently found in the biosynthesis of primary and secondary metabolites. Decarboxylase enzymes responsible for these transformations operate via diverse mechanisms and act on a large variety of substrates, making them appealing in terms of biotechnological applications. This Perspective focuses on the occurrence of decarboxylation reactions in natural product biosynthesis and provides a perspective on their applications in biocatalysis for fine chemicals and pharmaceuticals.

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.

Enhancing ferryl accumulation in H2O2-dependent cytochrome P450s

A facile strategy is presented to enhance the accumulation of ferryl (iron(IV)-oxo) species in H2O2 dependent cytochrome P450s (CYPs) of the CYP152 family. We report the characterization of a highly chemoselective CYP decarboxylase from Staphylococcus aureus (OleTSA) that is soluble at high concentrations. Examination of OleTSA Compound I (CpdI) accumulation with a variety of fatty acid substrates reveals a dependence on resting spin-state equilibrium. Alteration of this equilibrium through targeted mutagenesis of the proximal pocket favors the high-spin form, and as a result, enhances Cpd-I accumulation to nearly stoichiometric yields.