Kinase inhibitor pulldown assay (KiP) for clinical proteomics.

Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method. Data are available via ProteomeXchange with identifiers PXD044655 and PXD046169.

Usefulness of magnetic resonance imaging characteristics in discriminating H3 K27M-mutant gliomas from wildtype gliomas in spinal cord.

AIM: The aim of this study was to determine the usefulness of magnetic resonance imaging (MRI) characteristics in discriminating H3 K27M-mutant gliomas from wildtype gliomas in the spinal cord. MATERIALS AND METHODS: Fifty-eight patients with spinal cord gliomas were enrolled in this study. The H3 K27 gene status was identified by Sanger sequencing or immunohistochemistry test of resection tumor specimens. The MR imaging characteristics were evaluated and compared between H3 K27M-mutant and wildtype gliomas using the χ2 test and the Mann-Whitney U test. RESULTS: Of 58 recruited patients, 23 (39.7%) were diagnosed with H3 K27M-mutant glioma. The H3 K27M-mutant gliomas were found to more likely occur in men compared with wildtype gliomas (87.0% vs. 42.9%, p = 0.001). On T2-weighted MR images, the signal-to-noise ratio (SNR) of H3 K27M-mutant gliomas was significantly lower than that of wildtype gliomas (103.9 ± 72.0 vs. 168.9 ± 86.8, p < 0.001). Of 35 wildtype tumors, 60% showed well-defined margin but this feature was not found in all mutant tumors (p < 0.001). The SNR of tumors on contrast-enhanced T1-weighted images of the H3 K27M-mutant gliomas was significantly lower than that of wildtype gliomas (187.7 ± 160.4 vs. 295.1 ± 207.8, p = 0.006). Receiver operating-characteristic analysis revealed that area under curve (AUC) of combination of 1/SNR on T2-weighted images, 1/SNR on contrast-enhanced T1-weighted images, ill-defined margin, and sex reached 0.937 (95% CI, 0.873-1.000) in discriminating H3 K27M-mutant gliomas. CONCLUSIONS: The MR imaging characteristics are valuable in discriminating H3 K27M-mutant from wildtype gliomas in the spinal cord and the combination of these imaging features with sex had a high strength in this discrimination.

The risk paradox: Exploring asymmetric nexus between climate policy uncertainty and renewable energy technology budgets.

The ups and downs of climate policy uncertainty (CPU) cast a captivating shadow over the budgets allocated to renewable energy (RE) technologies, where strategic choices and risk assessment will determine the course of our green environmental revolution. The main intention of this investigation is to scrutinize the effect of CPU on the RE technology budgets (RETBs) in the top 10 countries with the highest RE research and development budgets (the USA, China, South Korea, India, Germany, the United Kingdom, France, Japan, Australia, and Italy). Although former researchers have typically employed panel data tools to contemplate the connection between CPU and RE technology, they repeatedly ignored variations in this connection throughout different economies. In contrast, our research adopts a unique approach, "quantile-on-quantile," to check this association at the country-to-country level. This approach offers a comprehensive worldwide perspective while procuring tailor-made perceptions for individual economies. The outcomes suggest that CPU significantly decreases RETBs across several data quantiles in our sample nations. In addition, the outcomes underscore that the connections between our variables differ among nations. These outcomes highlight the significance of policymakers implementing thorough appraisals and skillfully governing plans relevant to CPU and RETBs.

Rapid chemical reduction synthesis of copper nanoclusters with blue fluorescence for highly sensitive detection of furazolidone.

Tannic acid (TA), as a stabilizing agent, was successfully utilized to establish blue-emitting copper nanoclusters (TA-Cu NCs) on the basis of a facile chemical reduction preparation method. Characterization results proved successful synthesis of TA-Cu NCs with uniform size and excellent stability. TA-Cu NCs exhibited a blue emission wavelength at 431 nm when excited at 364 nm. Interestingly, the as-prepared TA-Cu NCs were selectively quenched by furazolidone based on static quenching. In addition, this analysis platform for furazolidone detection had an excellent linear range from 0.5 to 120 µM with a detection limit of 0.074 µM (S/N = 3). Furthermore, the accuracy of this sensing method was successfully confirmed by detecting furazolidone in bovine serum samples, indicating that TA-Cu NCs had bright application prospects.

Human placenta-derived mesenchymal stem cell administration protects against acute lung injury in a mouse model.

This study aims to investigate the effect of placenta-derived mesenchymal stem cells (PMSCs) administration on tissue repair following acute lung injury (ALI). PMSCs were transplanted intravenously to a mouse model of lipopolysaccharide-induced ALI. The therapeutic effects were determined by evaluating several indicators, including pathology; the wet/dry ratio of the lungs; blood gas analysis; the total protein content, cell numbers, and the activity of myeloperoxidase (MPO) in bronchial alveolar lavage fluid (BALF); and the levels of anti-inflammatory and proinflammatory cytokines in serum and BALF. To investigate the underlying mechanism, PMSC-derived exosomes were used for ALI treatment. Administration of PMSCs improved the degree of lung injury, reduced inflammation, increased the expression levels of anti-inflammatory cytokines, and protected lung function. As expected, the effects of PMSC-derived exosomes in the ALI model were similar to those of PMSCs, both in terms of improved lung function and reduced inflammation. These findings suggest that PMSCs have ameliorating effects on ALI that are potentially mediated via their secreted exosomes.

Single-Atom Pd-N4 Catalysis for Stable Low-Overpotential Lithium-Oxygen Battery.

The critical challenge for Li-O2 batteries lies in the large charge overpotential, leading to undesirable side reactions and inferior cycle stability. Single-atom catalysts have shown promising prospects in expediting the kinetics of oxygen evolution reaction (OER) for Li-O2 batteries. However, a present practical drawback is the limited understanding of the correlation between the unique atomic structures and the OER mechanism. Herein, a template-assisted strategy is reported to synthesize atomically dispersed Pd anchored on N-doped carbon spheres as cathode catalysts. Benefiting from the well-defined Pd-N4 moiety, the morphology and distribution of Li2 O2 products are distinctly regulated with optimized decomposition reversibility. Theoretical simulations reveal that the unique configuration of Pd-N4 will contribute to the electron transfer from Pd atoms to the adjacent N atoms, which turns the originally electroneutral Pd into positively charged and downshifts the d-band center and therefore weakens its adsorption energy with the intermediates. The Li-O2 batteries with Pd SAs/NC cathode achieve a charge overpotential of only 0.24 V and sustainable low-overpotential cycling stability (500 mA g-1 ), and can retain a low charge voltage to a very high capacity of 10 000 mAh g-1 . This work provides some insights into designing efficient single-atom catalysts for stable low-overpotential Li-O2 batteries.

Water-Trapping Single-Atom Co-N4 /Graphene Triggering Direct 4e- LiOH Chemistry for Rechargeable Aprotic Li-O2 Batteries.

Lithium-oxygen (Li-O2 ) batteries have received extensive attention owing to ultrahigh theoretical energy density. Compared to typical discharge product Li2 O2 , LiOH has attracted much attention for its better chemical and electrochemical stability. Large-scale applications of Li-O2 batteries with LiOH chemistry are hampered by the serious internal shuttling of the water additives with the desired 4e- electrochemical reactions. Here, a metal organic framework-derived "water-trapping" single-atom-Co-N4 /graphene catalyst (Co-SA-rGO) is provided that successfully mitigates the water shuttling and enables the direct 4e- catalytic reaction of LiOH in the aprotic Li-O2 battery. The Co-N4 center is more active toward proton-coupled electron transfer, benefiting - direction 4e- formation of LiOH. 3D interlinked networks also provide large surface area and mesoporous structures to trap ≈12 wt% H2 O molecules and offer rapid tunnels for O2 diffusion and Li+ transportation. With these unique features, the Co-SA-rGO based Li-O2 battery delivers a high discharge platform of 2.83 V and a large discharge capacity of 12 760.8 mAh g-1 . Also, the battery can withstand corrosion in the air and maintain a stable discharge platform for 220 cycles. This work points out the direction of enhanced electron/proton transfer for the single-atom catalyst design in Li-O2 batteries.

Head-to-head comparison of prostate-specific membrane antigen PET and multiparametric MRI in the diagnosis of pretreatment patients with prostate cancer: a meta-analysis.

OBJECTIVES: To compare prostate-specific membrane antigen (PSMA) PET with multiparametric MRI (mpMRI) in the diagnosis of pretreatment prostate cancer (PCa). METHODS: Pubmed, Embase, Medline, Web of Science, and Cochrane Library were searched for eligible studies published before June 22, 2022. We assessed risk of bias and applicability by using QUADAS-2 tool. Data synthesis was performed with Stata 17.0 software, using the "midas" and "meqrlogit" packages. RESULTS: We included 29 articles focusing on primary cancer detection, 18 articles about primary staging, and two articles containing them both. For PSMA PET versus mpMRI in primary PCa detection, sensitivities and specificities in the per-patient analysis were 0.90 and 0.84 (p<0.0001), and 0.66 and 0.60 (p <0.0001), and in the per-lesion analysis they were 0.79 and 0.78 (p <0.0001), and 0.84 and 0.82 (p <0.0001). For the per-patient analysis of PSMA PET versus mpMRI in primary staging, sensitivities and specificities in extracapsular extension detection were 0.59 and 0.66 (p =0.005), and 0.79 and 0.76 (p =0.0074), and in seminal vesicle infiltration (SVI) detection they were 0.51 and 0.60 (p =0.0008), and 0.93 and 0.96 (p =0.0092). For PSMA PET versus mpMRI in lymph node metastasis (LNM) detection, sensitivities and specificities in the per-patient analysis were 0.68 and 0.46 (p <0.0001), and 0.91 and 0.90 (p =0.81), and in the per-lesion analysis they were 0.67 and 0.36 (p <0.0001), and 0.99 and 0.99 (p =0.18). CONCLUSION: PSMA PET has higher diagnostic value than mpMRI in the detection of primary PCa. Regarding the primary staging, mpMRI has potential advantages in SVI detection, while PSMA PET has relative advantages in LNM detection. CLINICAL RELEVANCE STATEMENT: The integration of prostate-specific membrane antigen (PSMA) PET into the diagnostic pathway may be helpful for improving the accuracy of prostate cancer detection. However, further studies are needed to address the cost implications and evaluate its utility in specific patient populations or clinical scenarios. Moreover, we recommend the combination of PSMA PET and mpMRI for cancer staging. KEY POINTS: • Prostate-specific membrane antigen PET has higher sensitivity and specificity for primary tumor detection in prostate cancer compared to multiparametric MRI. • Prostate-specific membrane antigen PET also has significantly better sensitivity and specificity for lymph node metastases of prostate cancer compared to multiparametric MRI. • Multiparametric MRI has better accuracy for extracapsular extension and seminal vesicle infiltration compared to ate-specific membrane antigen PET.

Lithium storage performance enhanced by lithiation-induced structural phase transitions of fluorinated MXenes.

Structural phase transitions in electrode materials of Li-ion batteries (LIBs) often occur along with Li-ion extraction/intercalation during charge and discharge processes. Lithiation-induced phase transition behaviors of two-dimensional fluorinated MXenes were investigated systematically by first-principles density functional calculations. The calculated results show that fluorine atoms in the nine MXenes studied moved from the FCC site (or HCP site for Ta2CF2) to the TOP site during Li adsorption. Further all the predicted phase transitions were confirmed by ab initio molecular dynamic simulations. The band structure, density of state, diffusion energy barrier, average voltage and storage capacity were calculated to evaluate the lithium storage properties of fluorinated MXenes, which revealed that V2CF2 and Ti2CF2 are the optimal candidates for LIB electrode materials. The structural phase transition led to improvements in the cycle stability, storage capacity, average voltage, and other lithium storage properties of the fluorinated MXenes.

A systematic computational investigation of lithiation-induced structural phase transitions of O-functionalized MXenes.

Along with Li-ion extraction/intercalation during charge and discharge processes, structural phase transitions often occur in the electrode materials of Li-ion batteries (LIBs). By determining atomic positions before and after Li adsorptions, structural phase transitions of two-dimensional MXenes were investigated systematically using first-principles density functional calculations. The lithiation-induced phase transitions of ten M2C MXenes with oxygen groups can be divided into three types. No phase transitions occur for Ti-type MXenes including Ti2CO2, Zr2CO2 and Hf2CO2. The oxygens in Ta-type MXenes (Sc2CO2, Y2CO2, Nb2CO2 and Ta2CO2) move from one type of octahedral void to another type of octahedral void. However, for Mo-type MXenes including V2CO2, Cr2CO2 and Mo2CO2, the oxygens move from octahedral voids to tetrahedral voids. The mechanisms whether phase transitions happen or not are dependent on the sizes of M ions. Furthermore, all the predicted phase transitions were confirmed by ab initio molecular dynamics simulations. The calculated results of electron localization functions and Bader charge illustrate that there exist strong Coulomb interactions (ionic bonds) between Li and MXene surfaces. The band structure, diffusion energy barrier, open circuit voltage and storage capacity were calculated to evaluate the lithium storage properties of different MXenes, which reveals that V2CO2 and Cr2CO2 should be optimal candidates as electrode materials for LIBs.

LRRK2 mediates axon development by regulating Frizzled3 phosphorylation and growth cone-growth cone communication.

Axon-axon interactions are essential for axon guidance during nervous system wiring. However, it is unknown whether and how the growth cones communicate with each other while sensing and responding to guidance cues. We found that the Parkinson's disease gene, leucine-rich repeat kinase 2 (LRRK2), has an unexpected role in growth cone-growth cone communication. The LRRK2 protein acts as a scaffold and induces Frizzled3 hyperphosphorylation indirectly by recruiting other kinases and also directly phosphorylates Frizzled3 on threonine 598 (T598). In LRRK1 or LRRK2 single knockout, LRRK1/2 double knockout, and LRRK2 G2019S knockin, the postcrossing spinal cord commissural axons are disorganized and showed anterior-posterior guidance errors after midline crossing. Growth cones from either LRRK2 knockout or G2019S knockin mice showed altered interactions, suggesting impaired communication. Intercellular interaction between Frizzled3 and Vangl2 is essential for planar cell polarity signaling. We show here that this interaction is regulated by phosphorylation of Frizzled3 at T598 and can be regulated by LRRK2 in a kinase activity-dependent way. In the LRRK1/2 double knockout or LRRK2 G2019S knockin, the dopaminergic axon bundle in the midbrain was significantly widened and appeared disorganized, showing aberrant posterior-directed growth. Our findings demonstrate that LRRK2 regulates growth cone-growth cone communication in axon guidance and that both loss-of-function mutation and a gain-of-function mutation (G2019S) cause axon guidance defects in development.

Involvement of the dorsal and ventral attention networks in visual attention span.

Visual attention span (VAS), which refers to the window size of multielement parallel processing in a short time, plays an important role in higher-level cognition (e.g., reading) as required by encoding large amounts of information input. However, it is still a matter of debate about the underlying neural mechanism of VAS. In the present study, a modified visual 1-back task was designed by using nonverbal stimuli and nonverbal responses, in which possible influences of target presence and position were considered to identify more pure VAS processing. A task-driven functional magnetic resonance imaging (fMRI) experiment was then performed, and 30 healthy adults participated in this study. Results of confirmatory and exploratory analyses consistently revealed that both dorsal attention network (DAN) and ventral attention network (VAN) were significantly activated during this visual simultaneous processing. In particular, more significant activation in the left superior parietal lobule (LSPL), as compared to that in the bilateral inferior frontal gyrus (IFGs), suggested a greater involvement of DAN in VAS-related processing in contrast to VAN. In addition, it was also found that the activation in temporoparietal junctions (TPJs) were suppressed during multielement processing only in the target-absent condition. The current results suggested the recruitment of LSPL in covert attentional shifts and top-down control of VAS resources distribution during the rapid visual simultaneous processing, as well as the involvement of bilateral IFGs (especially RIFG) in both VAS processing and inhibitory control. The present findings might bring some enlightenments for diagnosis of the atypicality of attentional disorders and reading difficulties.

The key to improving the performance of Li-air batteries: recent progress and challenges of the catalysts.

Li-air batteries are considered to be one of the most promising energy storage devices due to their high energy density and large specific capacity. But the high overpotential, the sluggish oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) kinetics, and the poor cycling stability critically restrict their practical applications. To overcome these problems, various catalysts and electrolyte mediators have been used and studied. However, for practical application, these catalysts still have some challenges and scientific problems that need to be solved. Specifically, the performance of lithium-air batteries faces three major problems of capacity, overpotential, and cycle life that need to be solved. Solid-phase catalysts and liquid-phase redox mediators have their own advantages and disadvantages in the performance and reaction mechanism of lithium-air batteries. This review comprehensively analyzes and summarizes the catalytic materials and electrolyte additives of different systems and discusses in depth the corresponding reaction mechanism and performance (including technical characteristics and application difficulty). Finally, according to the characteristics of catalysts and practical application difficulties, the development direction of lithium-air batteries is proposed. Li-air batteries need to exploit the advantages of catalysts and redox mediators in terms of stability and overpotential to improve the electrochemical performance of the battery. In the future, anode protection and air purification systems will be combined to achieve large-scale, long-cycle applications of lithium-air batteries.

A feasible biochar derived from biogas residue and its application in the efficient adsorption of tetracycline from an aqueous solution.

The recovery of carbon materials from biogas residue (BR) could efficiently promote the efficient utilization of waste and the preparation of novel materials. In this study, a green and feasible reagent of citric acid was introduced and applied in the modification of biogas residue biochar (BRC). The modified biogas residue biochar (CABRC) showed a superior adsorption ability due to its higher specific surface area (approximately 6 times that of the BRC). Additionally, the adsorption capacities of CABRC and BRC for TC were 58.25 mg/g and 20.77 mg/g, respectively, while the TC adsorption performance of CABRC was 2.8 times that of BRC. The adsorption of TC by both BRC and CABRC was primarily controlled by physical adsorption and chemical adsorption (including pore filling, hydrogen bonding, π-π DEA interaction, and electrostatic interaction). Therefore, CABRC should be considered an environmentally friendly material due to its higher adsorption performance, which could expand its application in wastewater treatment.

Controllable Disulfide Exchange Polymerization of Polyguanidine for Effective Biomedical Applications by Thiol-Mediated Uptake.

New preparation methods of vectors are the key to developing the next generation of biomacromolecule delivery systems. In this study, a controllable disulfide exchange polymerization was established to obtain low-toxicity and efficient bioreducible polyguanidines (mPEG225 -b-PSSn , n=13, 26, 39, 75, 105) by regulating the concentration of activated nucleophiles and reaction time under mild reaction conditions. The relationship between the degrees of polymerization and biocompatibility was studied to identify the optimal polyguanidine mPEG225 -b-PSS26 . Such polyguanidine exhibited good in vitro performance in delivering different functional nucleic acids. The impressive therapeutic effects of mPEG225 -b-PSS26 were further verified in the 4T1 tumor-bearing mice as well as the mice with full-thickness skin defects. Controllable disulfide exchange polymerization provides an attractive strategy for the construction of new biomacromolecule delivery systems.

N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement.

The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the FeII-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent FeIV═O species. In the catalytic reaction pathway, the O2 binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the Cε-Nω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.

Targeting SOX2 Protein with Peptide Aptamers for Therapeutic Gains against Esophageal Squamous Cell Carcinoma.

Esophageal squamous cell carcinoma (ESCC) is a predominant cancer type in developing countries such as China, where ESCC accounts for approximately 90% of esophageal malignancies. Lacking effective and targeted therapy contributes to the poor 5-year survival rate. Recent studies showed that about 30% of ESCC cases have high levels of SOX2. Herein, we aim to target this transcription factor with aptamer. We established a peptide aptamer library and then performed an unbiased screening to identify several peptide aptamers including P42 that can bind and inhibit SOX2 downstream target genes. We further found that P42 overexpression or incubation with a synthetic peptide 42 inhibited the proliferation, migration, and invasion of ESCC cells. Moreover, peptide 42 treatment inhibited the growth and metastasis of ESCC xenografts in mouse and zebrafish. Further analysis revealed that P42 overexpression led to alternations in the levels of proteins that are important for the proliferation and migration of ESCC cells. Taken together, our study identified the peptide 42 as a key inhibitor of SOX2 function, reducing the proliferation and migration of ESCC cells in vitro and in vivo, and thereby offering a potential therapy against ESCC.

DPYSL3 modulates mitosis, migration, and epithelial-to-mesenchymal transition in claudin-low breast cancer.

A Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomic analysis prioritized dihydropyrimidinase-like-3 (DPYSL3) as a multilevel (RNA/protein/phosphoprotein) expression outlier specific to the claudin-low (CLOW) subset of triple-negative breast cancers. A PubMed informatics tool indicated a paucity of data in the context of breast cancer, which further prioritized DPYSL3 for study. DPYSL3 knockdown in DPYSL3-positive ([Formula: see text]) CLOW cell lines demonstrated reduced proliferation, yet enhanced motility and increased expression of epithelial-to-mesenchymal transition (EMT) markers, suggesting that DPYSL3 is a multifunctional signaling modulator. Slower proliferation in DPYSL3-negative ([Formula: see text]) CLOW cells was associated with accumulation of multinucleated cells, indicating a mitotic defect that was associated with a collapse of the vimentin microfilament network and increased vimentin phosphorylation. DPYSL3 also suppressed the expression of EMT regulators SNAIL and TWIST and opposed p21 activated kinase 2 (PAK2)-dependent migration. However, these EMT regulators in turn induce DPYSL3 expression, suggesting that DPYSL3 participates in negative feedback on EMT. In conclusion, DPYSL3 expression identifies CLOW tumors that will be sensitive to approaches that promote vimentin phosphorylation during mitosis and inhibitors of PAK signaling during migration and EMT.

Theoretical study on the catalytic mechanism of human deoxyhypusine hydroxylase.

Deoxyhypusine hydroxylase is a critical enzyme for hypusination of eukaryotic translation initiation factor 5A (eIF5A). Human deoxyhypusine hydroxylase (hDOHH) has a nonheme diiron active site that resembles both in structure and function of those found in methane and toluene monooxygenases, bacterial and mammalian ribonucleotide reductases, and stearoyl acyl carrier protein Δ9-desaturase from plants. However, the detailed catalytic mechanism of hDOHH is still unclear. In this work, extensive DFT calculations reveal that the catalytic mechanism of hDOHH consists of four consecutive steps: (1) peroxo isomerization triggered by substrate binding; (2) rate-determining O-O bond cleavage and formation of the [FeIV2(µ-O)2]4+ compound; (3) H atom abstraction from the substrate; and (4) OH rebound to the substrate. This work not only rationalizes the exceptional stability of the diiron(iii)-peroxo complex in hDOHH, but also confirms that hDOHH uses a diamond shape [FeIV2(µ-O)2]4+ core to complete crucial H atom abstraction from the substrate. Our DFT calculations exclude the reaction pathway of hDOHH to use diiron(iii)-peroxo species to directly react with the substrate.

Ruffling drives coproheme decarboxylation by facilitating PCET: a theoretical investigation of ChdC.

Coproheme decarboxylase (ChdC) is an essential enzyme in the coproporphyrin-dependent heme synthesis pathway, which catalyzes oxidative decarboxylation of coproheme at the positions p2 and p4 to generate heme b under the action of hydrogen peroxide. A mysterious characteristic of catalytic mechanism of ChdC is that both of the two decarboxylation sites are located remotely from the iron center of coproheme, which binds with hydrogen peroxide. By using density functional theory calculations, we have studied the coproheme decarboxylation mechanism of ChdC in detail. The calculation results show that in the first step of the catalytic reaction, H2O2 homolysis takes place synergistically with the proton coupled electron transfer process of a tyrosine (Tyr145) residing near p2 propionate. The produced reactive Tyr radical then abstracts a hydrogen atom from the ß carbon of the p2 propionate side chain, which is the rate-limiting step of the whole reaction with a 19.16 kcal mol-1 energy barrier. Finally, through intramolecular electron and proton rearrangement of coproporphyrin, decarboxylation of p2 propionate is accomplished. Our study revealed that the ruffled conformation of coproheme in ChdC is an important structural factor, which facilitates the decarboxylation reaction. We also found that the hydrogen bond chain located below the coproheme ring plays a role to regulate the PCET process of Tyr145. In addition, molecular dynamics simulations discovered that Lys149 is responsible for stabilizing the harderoheme III and positioning the second decarboxylation site p4 to the catalytic Tyr145 site in the decarboxylation reaction of the p4 site.