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Abstract DNA methylation at cytosine bases of eukaryotic DNA (5-methylcytosine, 5mC) is a heritable epigenetic mark that can regulate gene expression in health and disease. Enzymes that metabolize 5mC have been well-characterized, yet the discovery of endogenously produced signaling molecules that regulate DNA methyl-modifying machinery have not been described. Herein, we report that the free radical signaling molecule nitric oxide (NO) can directly inhibit the Fe(II)/2-OG-dependent DNA demethylases ten-eleven translocation (TET) and human AlkB homolog 2 (ALKBH2). Physiologic NO concentrations reversibly inhibited TET and ALKBH2 demethylase activity by binding to the mononuclear non-heme iron atom which formed a dinitrosyliron complex (DNIC) preventing cosubstrates (2-OG and O₂) from binding. In cancer cells treated with exogenous NO, or cells endogenously synthesizing NO, there was a global increase in 5mC and 5-hydroxymethylcytosine (5hmC) in DNA, the substrates for TET, that could not be attributed to increased DNA methyltransferase activity. 5mC was also elevated in NO-producing cell-line-derived mouse xenograft and patient-derived xenograft tumors. Genome-wide DNA methylome analysis of cells chronically treated with NO (10 days) demonstrated enrichment of 5mC and 5hmC at gene-regulatory loci which correlated to changes in the expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a novel epigenetic role for NO. 

ABSTRACT Polyketide synthases (PKSs) are multi-domain enzymatic assembly lines that biosynthesise a wide selection of bioactive natural products from simple building blocks. In contrast to theircis-acyltransferase (AT) counterparts,trans-AT PKSs rely on stand-alone AT domains to load extender units onto acyl carrier protein (ACP) domains embedded in the core PKS machinery.Trans-AT PKS gene clusters also encode acyl hydrolase (AH) domains, which are predicted to share the overall fold of AT domains, but hydrolyse aberrant acyl chains from ACP domains, thus ensuring efficient polyketide biosynthesis. How such domains specifically target short acyl chains, in particular acetyl groups, tethered as thioesters to the substrate-shuttling ACP domains, with hydrolytic rather than acyl transfer activity, has remained unclear. To answer these questions, we solved the first structure of an AH domain and performed structure-guided activity assays on active site variants. Our results offer key insights into chain length control and selection against coenzyme A-tethered substrates, and clarify how the interaction interface between AH and ACP domains contributes to recognition of cognate and non-cognate ACP domains. Combining our experimental findings with molecular dynamics simulations allowed for the production of a data-driven model of an AH:ACP domain complex. Our results advance the currently incomplete understanding of polyketide biosynthesis bytrans-AT PKSs, and provide foundations for future bioengineering efforts. 

Abstract The electrocatalytic reduction of molecular nitrogen to ammonia—the nitrogen reduction reaction (NRR)—is of broad interest as an environmentally- and energy-friendly alternative to the Haber–Bosch process for agricultural and emerging energy applications. Herein, we review our recent findings from collaborative electrochemistry/surface science/theoretical studies that counter several commonly held assumptions regarding transition metal oxynitrides and oxides as NRR catalysts. Specifically, we find that for the vanadium oxide, vanadium oxynitride, and cobalt oxynitride systems, (a) there is no Mars–van Krevelen mechanism and that the reduction of lattice nitrogen and N₂to NH₃occurs by parallel reaction mechanisms at O-ligated metal sites without incorporation of N into the oxide lattice; and (b) that NRR and the hydrogen evolution reaction do occur in concert under the conditions studied for Co oxynitride, but not for V oxynitride. Additionally, these results highlight the importance of both O-ligation of the V or Co center for metal-binding of dinitrogen, and the importance of N in stabilizing the transition metal cation in an intermediate oxidation state, for effective N≡N bond activation. This review also highlights the importance and limitations ofex situandin situphotoemission—involving controlled transfer between ultra-high vacuum and electrochemistry environments, and ofoperandonear ambient pressure photoemission coupled within situstudies, in elucidating the complex chemistry relevant to the electrolyte/solid interface. 

Nonsymmetrical oxygen-bridged binuclear copper centers have been proposed and modeled as intermediates and transition states in several C─H oxidation pathways, leading to the postulation that structural dissymmetry enhances the reactivity of the bridging oxygen. However, experimentally characterizing the structure and reactivity of these transient species is remarkably challenging. Here, we report the high-pressure synthesis of a metastable nonsymmetrical dicopper-μ-oxo compound with exceptional reactivity toward the mono-oxygenation of aliphatic C─H bonds. The nonequivalent coordination environment of copper stabilizes localized mixed valency and greatly enhances the hydrogen atom abstraction activity of the bridging oxygen, enabling room-temperature hydroxylation of methane under pressure. These findings highlight the role of dissymmetry in the reactivity of binuclear copper centers and demonstrate precise control of molecular structures by mechanical means. 

The electrochemical reduction of nitrate to ammonia is of interest as an energy/environmentally friendly source of ammonia for agriculture and energy applications and as a route toward groundwater purification. We report in situ photoemission data, electrochemical results, and density functional theory calculations that demonstrate vanadium oxide—prepared by ambient exposure of V metal, with a distribution of surface V³⁺and V⁴⁺oxidation states—specifically adsorbs and reduces nitrate to ammonia at pH 3.2 at cathodic potentials. Negligible cathodic activity in the absence of NO₃⁻indicates high selectivity with respect to non-nitrate reduction processes. In situ photoemission data indicate that nitrate adsorption and reduction to adsorbed NO₂is a key step in the reduction process. NO₃RR activity is also observed at pH 7, albeit at a much slower rate. The results indicate that intermediate (non-d⁰) oxidation states are important for both molecular nitrogen and nitrate reduction to ammonia. 

Reversible cyclopropane formation is examined in a chromium diamide–diimine chelate complexviareduction. Sites of electrophilicity incur similar and divergent chemistry; structural, electrochemical, and calculational studies afford their rationale. 

The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2′-deoxycytidine 5′-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3′-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase. 

QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise. We showed that despite those limitations, polarizable and non-polarizable force fields can reproduce relative cooperativity achieved using density functional theory due to error compensation mechanisms. In this contribution, we assess the performance of QM/MM methods in reproducing these phenomena. Our study highlights the significance of the QM region size and force field choice in QM/MM calculations, emphasizing the importance of parameter validation to obtain accurate interaction energy predictions.