High-Resolution Crystal Structures Reveal Plasticity in the Metal Binding Site of Apurinic/Apyrimidinic Endonuclease I

Apurinic/apyrimidinic endonuclease I (APE1) is an essential base excision repair enzyme that catalyzes a Mg2+-dependent reaction in which the phosphodiester backbone is cleaved 5′ of an abasic site in duplex DNA. This reaction has been proposed to involve either one or two metal ions bound to the active site. In the present study, we report crystal structures of Mg2+, Mn2+, and apo-APE1 determined at 1.4, 2.2, and 1.65 Å, respectively, representing two of the highest resolution structures yet reported for APE1. In our structures, a single well-ordered Mn2+ ion was observed coordinated by D70 and E96; the Mg2+ site exhibited disorder modeled as two closely positioned sites coordinated by D70 and E96 or E96 alone. Direct metal binding analysis of wild-type, D70A, and E96A APE1, as assessed by differential scanning fluorimetry, indicated a role for D70 and E96 in binding of Mg2+ or Mn2+ to APE1. Consistent with the disorder exhibited by Mg2+ bound to the active site, two different conformations of E96 were observed coordinated to Mg2+. A third conformation for E96 in the apo structure is similar to that observed in the APE1–DNA–Mg2+ complex structure. Thus, binding of Mg2+ in three different positions within the active site of APE1 in these crystal structures corresponds directly with three different conformations of E96. Taken together, our results are consistent with the initial capture of metal by D70 and E96 and repositioning of Mg2+ facilitated by the structural plasticity of E96 in the active site

Discovery of macrocyclic inhibitors of apurinic/apyrimidinic endonuclease 1

Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential base excision repair enzyme that is upregulated in a number of cancers, contributes to resistance of tumors treated with DNA-alkylating or -oxidizing agents, and has recently been identified as an important therapeutic target. In this work, we identified hot spots for binding of small organic molecules experimentally in high resolution crystal structures of APE1 and computationally through the use of FTMAP analysis (http://ftmap.bu.edu/). Guided by these hot spots, a library of drug-like macrocycles was docked and then screened for inhibition of APE1 endonuclease activity. In an iterative process, hot-spot-guided docking, characterization of inhibition of APE1 endonuclease, and cytotoxicity of cancer cells were used to design next generation macrocycles. To assess target selectivity in cells, selected macrocycles were analyzed for modulation of DNA damage. Taken together, our studies suggest that macrocycles represent a promising class of compounds for inhibition of APE1 in cancer cells.This work was supported by grants from the National Institutes of Health (Grant R01CA205166 to M.R.K. and M.M.G. and Grant R01CA167291 to M.R.K.) and by the Earl and Betty Herr Professor in Pediatric Oncology Research, Jeff Gordon Children's Foundation, and the Riley Children's Foundation (M.R.K.). Work at the BU-CMD (J.A.P., L.E.B., R.T.) is supported by the National Institutes of Health, Grant R24 GM111625. D.B. and S.V. were supported by the National Institutes of Health, Grant R35 GM118078. (R35 GM118078 - National Institutes of Health; R01CA205166 - National Institutes of Health; R01CA167291 - National Institutes of Health; R24 GM111625 - National Institutes of Health; Earl and Betty Herr Professor in Pediatric Oncology Research; Jeff Gordon Children's Foundation; Riley Children's Foundation)Accepted manuscriptSupporting documentatio

Characterization of the redox activity and disulfide bond formation in Apurinic/apyrimidinic endonuclease

Apurinic/apyrimidinic endonuclease (APE1) is an unusual nuclear redox factor in which the redox-active cysteines identified to date, C65 and C93, are surface inaccessible residues whose activities may be influenced by partial unfolding of APE1. To assess the role of the five remaining cysteines in APE1’s redox activity, double-cysteine mutants were analyzed, excluding C65A, which is redox-inactive as a single mutant. C93A/C99A APE1 was found to be redox-inactive, whereas other double-cysteine mutants retained the same redox activity as that observed for C93A APE1. To determine whether these three cysteines, C65, C93, and C99, were sufficient for redox activity, all other cysteines were substituted with alanine, and this protein was shown to be fully redox-active. Mutants with impaired redox activity failed to stimulate cell proliferation, establishing an important role for APE1’s redox activity in cell growth. Disulfide bond formation upon oxidation of APE1 was analyzed by proteolysis of the protein followed by mass spectrometry analysis. Within 5 min of exposure to hydrogen peroxide, a single disulfide bond formed between C65 and C138 followed by the formation of three additional disulfide bonds within 15 min; 10 total disulfide bonds formed within 1 h. A single mixed-disulfide bond involving C99 of APE1 was observed for the reaction of oxidized APE1 with thioredoxin (TRX). Disulfide-bonded APE1 or APE1–TRX species were further characterized by size exclusion chromatography and found to form large complexes. Taken together, our data suggest that APE1 is a unique redox factor with properties distinct from those of other redox factors

A review of enhancement of biohydrogen productions by chemical addition using a supervised machine learning method

In this work, the impact of chemical additions, especially nano‐particles (NPs), was quan-titatively analyzed using our constructed artificial neural networks (ANNs)‐response surface methodology (RSM) algorithm. Fe‐based and Ni‐based NPs and ions, including Mg2+, Cu2+, Na+, NH4+, and K+, behave differently towards the response of hydrogen yield (HY) and hydrogen evolution rate (HER). Manipulating the size and concentration of NPs was found to be effective in enhancing the HY for Fe‐based NPs and ions, but not for Ni‐based NPs and ions. An optimal range of particle size (86–120 nm) and Ni‐ion/NP concentration (81–120 mg L−1) existed for HER. Meanwhile, the manipulation of the size and concentration of NPs was found to be ineffective for both iron and nickel for the improvement of HER. In fact, the variation in size of NPs for the enhancement of HY and HER demonstrated an appreciable difference. The smaller (less than 42 nm) NPs were found to definitely improve the HY, whereas for the HER, the relatively bigger size of NPs (40–50 nm) seemed to significantly increase the H2 evolution rate. It was also found that the variations in the concentration of the investigated ions only statistically influenced the HER, not the HY. The level of response (the enhanced HER) towards inputs was underpinned and the order of significance towards HER was identified as the following: Na+ \u3e Mg2+ \u3e Cu2+ \u3e NH4+ \u3e K+

Three-Dimensional Manganese Oxide@Carbon Networks as Free-Standing, High-Loading Cathodes for High-Performance Zinc-Ion Batteries

Zinc-ion batteries (ZIBs), which are inexpensive and environmentally friendly, have a lot of potential for use in grid-scale energy storage systems, but their use is constrained by the availability of suitable cathode materials. MnO2-based cathodes are emerging as a promising contenders, due to the great availability and safety, as well as the device's stable output voltage platform (1.5 V). Improving the slow kinetics of MnO2-based cathodes caused by low electrical conductivity and mass diffusion rate is a challenge for their future use in next-generation rapid charging devices. Herein, the aforementioned challenges are overcome by proposing a sodium-intercalated manganese oxide (NMO) with 3D varying thinness carbon nanotubes (VTCNTs) networks as appropriate free-standing, binder-free cathodes (NMO/VTCNTs) without any heat treatment. A network construction strategy based on CNTs of different diameters is proposed for the first time to provide high specific capacity while achieving high mass loading. The specific capacity of as-prepared cathodes is significantly increased. The resulting free-standing binder-free cathodes achieve excellent capacity (329 mAh g−1 after 120 cycles at 0.2 A g−1 and 225 mAh g−1 after 200 cycles at 1 A g−1) and long-term cycling stability (158 mAh g−1 at 2 A g−1 after 1000 cycles)

Three-Dimensional Manganese Oxide@Carbon Networks as Free-Standing, High-Loading Cathodes for High-Performance Zinc-Ion Batteries

Zinc-ion batteries (ZIBs), which are inexpensive and environmentally friendly, have a lot of potential for use in grid-scale energy storage systems, but their use is constrained by the availability of suitable cathode materials. MnO2-based cathodes are emerging as a promising contenders, due to the great availability and safety, as well as the device's stable output voltage platform (1.5 V). Improving the slow kinetics of MnO2-based cathodes caused by low electrical conductivity and mass diffusion rate is a challenge for their future use in next-generation rapid charging devices. Herein, the aforementioned challenges are overcome by proposing a sodium-intercalated manganese oxide (NMO) with 3D varying thinness carbon nanotubes (VTCNTs) networks as appropriate free-standing, binder-free cathodes (NMO/VTCNTs) without any heat treatment. A network construction strategy based on CNTs of different diameters is proposed for the first time to provide high specific capacity while achieving high mass loading. The specific capacity of as-prepared cathodes is significantly increased. The resulting free-standing binder-free cathodes achieve excellent capacity (329 mAh g−1 after 120 cycles at 0.2 A g−1 and 225 mAh g−1 after 200 cycles at 1 A g−1) and long-term cycling stability (158 mAh g−1 at 2 A g−1 after 1000 cycles)

When It's Heavier: Interfacial and Solvation Chemistry of Isotopes in Aqueous Electrolytes for Zn-ion Batteries

The electrochemical effect of isotope (EEI) of water is introduced in the Zn-ion batteries (ZIBs) electrolyte to deal with the challenge of severe side reactions and massive gas production. Due to the low diffusion and strong coordination of ions in D2O, the possibility of side reactions is decreased, resulting in a broader electrochemically stable potential window, less pH change, and less zinc hydroxide sulfate (ZHS) generation during cycling. Moreover, we demonstrate that D2O eliminates the different ZHS phases generated by the change of bound water during cycling because of the consistently low local ion and molecule concentration, resulting in a stable interface between the electrode and electrolyte. The full cells with D2O-based electrolyte demonstrated more stable cycling performance which displayed ∼100 % reversible efficiencies after 1,000 cycles with a wide voltage window of 0.8–2.0 V and 3,000 cycles with a normal voltage window of 0.8–1.9 V at a current density of 2 A g−1

Preparation and Characterization of New Nano-Composite Scaffolds Loaded With Vascular Stents

In this study, vascular stents were fabricated from poly (lactide-ɛ-caprolactone)/collagen/nano-hydroxyapatite (PLCL/Col/nHA) by electrospinning, and the surface morphology and breaking strength were observed or measured through scanning electron microscopy and tensile tests. The anti-clotting properties of stents were evaluated for anticoagulation surfaces modified by the electrostatic layer-by-layer self-assembly technique. In addition, nano-composite scaffolds of poly (lactic-co-glycolic acid)/polycaprolactone/nano-hydroxyapatite (PLGA/PCL/nHA) loaded with the vascular stents were prepared by thermoforming-particle leaching and their basic performance and osteogenesis were tested in vitro and in vivo. The results show that the PLCL/Col/nHA stents and PLGA/PCL/nHA nano-composite scaffolds had good surface structures, mechanical properties, biocompatibility and could guide bone regeneration. These may provide a new way to build vascularized-tissue engineered bone to repair large bone defects in bone tissue engineering

The Positive and Negative Synergistic Airflow-Type Jujube Fruit Harvester (P-N JH)

Low operation efficiency and poor working performance are the main reasons that restrict the application of pneumatic date pickers. In this study, it is proposed to use positive pressure air flow blowing and negative pressure air flow suction to pick jujube fruit and to use inertia air flow to remove impurities and design a positive and negative collaborative air flow type date fruit harvester (P-N JH). The second-order regression model of test factors and response indexes was established by using the central composite design method, and the operating performance of P-N JH was evaluated and comprehensively optimized, and the optimal combination of operating parameters was obtained: positive pressure wind speed, negative pressure wind speed, and travel speed were 16.8 m·s−1, 34.0 m·s−1, and 1.5 m·s−1, respectively. In addition, the verification test results show that the pickup rate, impurity rate, damage rate, and operating efficiency are 97.21%, 2.15%, 1.08%, and 2170 kg/h, respectively. The operating performance of P-N JH not only meets the requirements of jujube picking but also significantly improves the operating efficiency compared with the traditional air-suction jujube harvester. This study can provide theoretical and technical reference for the harvesting of air-suctioned dates; it also provides a new way of thinking for jujube fruit picking

Suppression of dendrite formation via ultrasonic stimulation

This research introduces a chemistry-agnostic approach to achieve rapid and degradation-free battery charging via ultrasonic agitation. An ultrasonic device operating in the megahertz range was used to stimulate electrolyte flow from outside the cell. The acoustic streaming effect accelerates ion transport from the bulk electrolyte to the electrode surface and suppresses the formation of an ion depletion zone. An experimental setup was used to optically observe the formation of dendrites when the current imposed across two zinc electrodes exceeded the limiting current. Beyond this limit, diffusion alone cannot provide sufficient ions, resulting in an ion depletion zone. It was subsequently shown that dendrite formation was reduced by over 98% when 15x the limiting current was forced across the electrodes and acoustic stimulation was delivered. Furthermore, it was shown that compared to the scenario without ultrasonic stimulation, the steady state potential was also reduced by 29%, indicating much better ion exchange between the electrodes. These findings suggest that ultrasonic stimulation can be a tool for enhancing electrochemical processes such as battery charging and discharging