Black Carbon Facilitated Dechlorination of DDT and its Metabolites by Sulfide

1,1-trichloro-2,2-di­(4-chlorophenyl)­ethane (DDT) and its metabolites 1,1-dichloro-2,2-bis­(4-chlorophenyl)­ethane (DDD) and 1,1-dichloro-2,2-bis­(4-chlorophenyl)­ethylene (DDE), are often detected in soils and sediments containing high concentrations of black carbon. Sulfide (∼5 mM) from biological sulfate reduction often coexists with black carbon and serves as both a strong reductant and a nucleophile for the abiotic transformation of contaminants. In this study, we found that the abiotic transformation of DDT, DDD, and DDE (collectively referred to as DDX) require both sulfide and black carbon. 89.3 ± 1.8% of DDT, 63.2 ± 1.9% of DDD, and 50.9 ± 1.6% of DDE were degraded by sulfide (5 mM) in the presence of graphite powder (21 g/L) after 28 days at pH 7. Chloride was a product of DDX degradation. To better understand the reaction pathways, electrochemical cells and batch reactor experiments with sulfide-pretreated graphite powder were used to differentiate the involvement of black carbon materials in DDX transformation by sulfide. Our results suggest that DDT and DDD are transformed by surface intermediates formed from the reaction between sulfide and black carbon, while DDE degradation involves reductive dechlorination. This research lays the groundwork for developing an alternative in situ remediation technique for rapidly decontaminating soils and sediments to lower toxic products under environmentally relevant conditions

Crystallographic and Biochemical Analysis of the Mouse Poly(ADP-Ribose) Glycohydrolase

<div><p>Protein poly(ADP-ribosyl)ation (PARylation) regulates a number of important cellular processes. Poly(ADP-ribose) glycohydrolase (PARG) is the primary enzyme responsible for hydrolyzing the poly(ADP-ribose) (PAR) polymer <i>in vivo</i>. Here we report crystal structures of the mouse PARG (mPARG) catalytic domain, its complexes with ADP-ribose (ADPr) and a PARG inhibitor ADP-HPD, as well as four PARG catalytic residues mutants. With these structures and biochemical analysis of 20 mPARG mutants, we provide a structural basis for understanding how the PAR polymer is recognized and hydrolyzed by mPARG. The structures and activity complementation experiment also suggest how the N-terminal flexible peptide preceding the PARG catalytic domain may regulate the enzymatic activity of PARG. This study contributes to our understanding of PARG catalytic and regulatory mechanisms as well as the rational design of PARG inhibitors.</p></div

A potential secondary <i>iso</i>-ADPr binding site.

<p>(a) A possible secondary binding site. <i>iso</i>-ADPr is showed in cyan stick. The bound <i>iso</i>-ADPr is close to the Exon4+5 encoded region (highlighted in black). (b) The 2Fo-Fc simulated annealed omit map of the potential secondary <i>iso</i>-ADPr binding region, calculated using the CNS package and contoured at 1.5σ. The <i>iso</i>-ADPr was omitted and simulated annealing was performed to remove model bias prior to electron density calculation. It is also apparent that the <i>iso</i>-ADPr molecule in this position is not restricted by crystal packing.</p

Mouse PARG catalytic domain apo- and ligand bound structures.

<p>(a) Overall structure of apo- mPARG(439–959). The protein is shown in rainbow and the N terminal MTS containing loop is in black. The cleft right in the middle is the active site. (b) ADPr bound mPARG structure. mPARG is shown in light orange and the ADPr is in cyan. Stereoview of key interactions involved in ADPr binding with the mPARG catalytic domain are shown in black dash lines. The key binding residues are highlighted in green sticks. (c) ADP-HPD bound mPARG structure. mPARG is shown in gray and the ADPr is in green. Stereoview of key interactions involved in ADP-HPD binding with the mPARG catalytic domain are shown in black dash lines. The key binding residues are highlighted in pink sticks. Aromatic rings of Tyr788 and Phe895 form perpendicular and parallel π stacking interactions with the adenine ring of ADPr or ADP-HPD, respectively. Tyr785 and Glu720 both form hydrogen bonds with the NH₂ group of the adenine ring. Thr718 and Ile719 are in close contact with the N1 of the adenine ring. In addition, Asn862 forms a hydrogen bond to 2′-OH of the adenine-linked ribose. Tyr788 also forms a hydrogen bond with one of the phosphates. (d) Superposition of unliganded mPARG (blue) and ADP-HPD bound mPARG (grey) structures.Three key loops are highlighted in red in ADP-HPD bound structure. Loop 2 undergoes conformational change to tightly pack the ADP-HPD. Both side chains of Phe868 and Phe895 (highlighted in grey sticks) rotate to strongly interact with ADP-HPD. (e) Superposition of ADP-HPD bound vertebrate PARG catalytic domains. ADP-HPD bound mPARG is in grey, ADP-HPD bound rPARG (PDB: 3UEL) is in wheat and ADP-HPD bound hPARG (PDB: 4B1J) is in magenta. ADP-HPD is showed in cyan stick.</p

Mutagenesis analysis of mPARG active site residues.

<p>(a) The active site of ADPr bound mPARG structure is shown in light orange. The ligand PAR is modeled in based on superposition of the ADPr bound mPARG structure with PAR bound <i>T. thermophila</i> PARG structure (PDB: 4L2H). PAR is shown in cyan stick, and the residues we designed for mutagenesis study are shown in pink stick. (b) 1 min and 1 h PARG TLC assay for wt mPARG and mutants. R478A, D480A,F491A and T493A are the mutants for the potential <i>iso</i>-ADPr binding sites, and the rest are the mutants for the active site. (c) Quantified PARG activity by 1 min PARG TLC assay for wt mPARG and mutants. The activities are normalized to wt mPARG. Error bars represent standard deviation (n = 3). (d) The signature loops of the wt mPARG and E748 and E749 mutants. Wt mPARG in blue; E748N in orange; E749N in magenta; E748Q in green; E749Q in cyan. The side chains for residues 748 and 749 are shown in sticks.</p

Quantitative Analysis of Histone Demethylase Probes Using Fluorescence Polarization

We previously reported methylstat as a selective inhibitor of jumonji C domain-containing histone demethylases (JHDMs). Herein, we describe the synthesis of a fluorescent analogue of methylstat and its application as a tracer in fluorescence polarization assays. Using this format, we have evaluated the binding affinities of several known JHDM probes, as well as the native cofactor and substrate of JHDM1A. This fluorophore allowed a highly robust and miniaturized competition assay sufficient for high-throughput screening

Strong Impacts of Regional Atmospheric Transport on the Vertical Distribution of Aerosol Ammonium over Beijing

Ammonium (NH4+) is a significant component of fine aerosol particles (PM2.5), and its behavior in the atmosphere is crucial to air pollution. We present a novel study that analyzes the vertical distribution and temporal trends of NH4+ in the urban boundary layer of Beijing, tracking hourly concentrations throughout a complete haze episode. Our results unveil a surprising single-peak profile of NH4+ at heights of 300–700 m in the urban boundary layer with its hourly concentration reaching ∼50 μg m–3, which is 3 times higher than that at the ground level, in contrast to the conventional patterns of decreasing concentrations with height. The vertical structure is closely related to the observed escape of ammonia (NH3) or NH4+ from upwind industrial sources via elevated chimneys. The NH4+ plumes emitted through these sources are prone to transport at an altitude of 270–750 m for approximately 6 h, covering >250 km to Beijing. This study reveals that non-agricultural point emissions of NH4+ impact the vertical patterns of aerosol NH4+ in the urban boundary layer, demonstrating potential opportunities for limiting such emission sources to curb PM2.5 pollution in the North China Plain

Strong Impacts of Regional Atmospheric Transport on the Vertical Distribution of Aerosol Ammonium over Beijing

Ammonium (NH4+) is a significant component of fine aerosol particles (PM2.5), and its behavior in the atmosphere is crucial to air pollution. We present a novel study that analyzes the vertical distribution and temporal trends of NH4+ in the urban boundary layer of Beijing, tracking hourly concentrations throughout a complete haze episode. Our results unveil a surprising single-peak profile of NH4+ at heights of 300–700 m in the urban boundary layer with its hourly concentration reaching ∼50 μg m–3, which is 3 times higher than that at the ground level, in contrast to the conventional patterns of decreasing concentrations with height. The vertical structure is closely related to the observed escape of ammonia (NH3) or NH4+ from upwind industrial sources via elevated chimneys. The NH4+ plumes emitted through these sources are prone to transport at an altitude of 270–750 m for approximately 6 h, covering >250 km to Beijing. This study reveals that non-agricultural point emissions of NH4+ impact the vertical patterns of aerosol NH4+ in the urban boundary layer, demonstrating potential opportunities for limiting such emission sources to curb PM2.5 pollution in the North China Plain