Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE b
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Smith, Kyle P.↗
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Structures of a synthetic antibody selected against and bound to the C‐terminal domain of Clostridium perfringens enterotoxin
Abstract Clostridium perfringensenterotoxin (CpE) causes cytotoxic gastrointestinal disease in mammalian epithelium by binding membrane protein receptors called claudins. Claudins direct the formation of cell/cell tight junctions through oligomerization and govern the transport of molecules between individual cells. CpE binds claudins through its C‐terminal domain (cCpE) and induces cytotoxicity through its N‐terminal domain. The non‐toxic cCpE is a useful tool to study claudins, tight junctions, and for translational applications, such as increasing the permeability of restrictive tissues like the blood–brain barrier or selective targeting of claudin overexpressing cancers. Conversely, there are no specialized molecular tools to study CpE or cCpE, or to modulate or inhibit their functions. We previously reported the development of synthetic antigen‐binding fragments (sFabs) that bind cCpE, and low‐resolution structures of them bound to claudin/cCpE complexes. Here, we determine high‐resolution structures of sFab COP‐2 bound to cCpE using X‐ray crystallography and cryogenic electron microscopy. The structures and biophysical findings provide the mechanism of COP‐2 binding to cCpE and the molecular determinants driving their interactions. These insights can advance the design of new antibody‐based tools from our COP‐2 scaffold to study or alter cCpE function and give rise to a “Trojan horse” strategy that exploits cCpE's tight junction barrier disrupting function to selectively deliver conjugated therapeutics through normally impermeable tissues.
Biochemistry & Molecular Biology↗
Nuclear Magnetic Resonance ‐based fragment screen of the E3 ligase Fem‐1 homolog B
Abstract Targeted protein degradation using PROTACs (PROteolysis TArgeting Chimeras) has emerged as a transformative therapeutic strategy, largely relying on a small number of E3 ubiquitin ligases such as CRBN and VHL. However, resistance, toxicity, and poor oral bioavailability limit the utility of PROTACs and highlight the need to expand the E3 ligase toolbox. Fem‐1 homolog B (FEM1B) is a lesser‐known E3 ligase that offers a promising alternative due to its broad expression and ability to recognize diverse degron motifs. Here, we describe the development of a stable construct of FEM1B, the results of a protein‐observed NMR‐based fragment screen using this construct, and the X‐ray structures of some of the fragment hits when bound to the protein. From these results, new PROTACs utilizing FEM1B as the E3 ligase may be discovered, providing an alternative E3 ligase for targeted protein degradation.
Katinas, Jade M. [Department of Biochemistry Vande↗
Synthesis, aphicidal activity and conformation of novel insect kinin analogues as potential eco‐friendly insecticides
Abstract BACKGROUND The discovery of ecofriendly insecticides through a new strategy for aphid control is important because of the substantial resistance and unexpected eco‐toxicity to honeybees caused by traditional insecticides. The insect kinins, a class of multifunctional insect neuropeptides, are considered for potential application in pest control. In our previous work we developed several series of insect kinin analogues and found a promising lead II‐1 with good aphicidal activity. To seek further eco‐friendly aphicides, the optimization of II‐1 is carried out in this study. RESULTS Fifteen novel Yaa 3 modified analogues based on the lead II‐1 were synthesized. The aphicidal tests indicated that IV‐3 , IV‐5 and IV‐10 exhibited significant activity against the soybean aphid Aphis glycines with LC 50 values of 0.0029, 0.0072 and 0.0086 mmol L –1 , respectively, higher than that of lead II‐1 and the commercial Pymetrozine. The molecular modeling results showed that analogues II‐1 , IV‐3 , IV‐5 , IV‐7 and IV‐10 formed a β‐turn‐like conformation, while the conformation of analogues IV‐1 , IV‐2 and IV‐9 seemed to be linear. Some structural elements favorable for the activity were proposed based on the conformation‐activity relationship of the analogues. CONCLUSION Insect kinin analogues derived from lead II‐1 by modifying the hydrolysis site Yaa 3 with natural, sterically hindered α‐ and β‐amino acids showed great potential as eco‐friendly insecticides. Inspiringly, the most active analogue IV‐3 can be a candidate for further development. The β‐turn‐like conformation and the orientation of the aromatic rings of the side chain of Phe 2 and Trp 4 may be critical factors beneficial to activity. © 2019 Society of Chemical Industry
Zhang, Chuanliang↗
Metal-Free, Oxidative Condensation of Heteroaryl- and Aryl Carbaldehydes towards Functionalized Carbonitriles
Functionalization of pyridines with the carbonitrile group for advanced cyclization reactions routinely incorporates metals, toxic oxidants, and cyanide reagents, often in linear synthetic sequences. Here, motivated by the strategic need of a heteroaryl carbonitrile synthon for further elaboration, we disclose an efficient, metal-free, one-pot reaction sequence that uses ammonium acetate as the nitrogen source and bis-acetoxyiodobenzene as the oxidant with low loadings. The developed method tolerates a diverse substrate scope including heteroaryl, aryl, and alkyl substrates with similar efficiency and expands the practitioner's reaction. Method development, optimization, substrate scope, preliminary mechanistic observations, competition experiments, and a scale up reaction are delineated herein.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Calcium–Based Metal–Organic Frameworks and Their Potential Applications
Metal–organic frameworks (MOFs) built on calcium metal (Ca-MOFs) represent a unique subclass of MOFs featuring high stability, low toxicity, and relatively low density. Ca-MOFs show considerable potential for molecular separations, electronic, magnetic, and biomedical applications, although they are not investigated as extensively as transition metal-based MOFs. Compared to MOFs made of other groups of metals, Ca-MOFs may be particularly advantageous for certain applications such as adsorption and storage of light molecules because of their gravimetric benefit, and drug delivery due to their high biocompatibility. This review intends to provide an overview on the recent development of Ca-MOFs, including their synthesis, crystal structures, important properties, and related applications. Here, various synthetic methods and techniques, types of building blocks, structure and porosity features, selected physical properties, and potential uses will be discussed and summarized. Representative examples will be illustrated for each type of important applications with a focus on their structure–property relations.
36 MATERIALS SCIENCE↗
Additive‐Free Aqueous MXene Inks for Thermal Inkjet Printing on Textiles
Abstract Direct printing of functional inks onto flexible substrates allows for scalable fabrication of wearable electronics. However, existing ink formulations for inkjet printing require toxic solvents and additives, which make device fabrication more complex, limit substrate compatibility, and hinder device performance. Even water‐based carbon or metal nanoparticle inks require supplemental surfactants, binders, and cosolvents to produce jettable colloidal suspensions. Here, a general approach is demonstrated for formulating conductive inkjet printable, additive‐free aqueous Ti 3 C 2 T x MXene inks for direct printing on various substrates. The rheological properties of the MXene inks are tuned by controlling the Ti 3 C 2 T x flake size and concentration. Ti 3 C 2 T x ‐based electrical conduits and microsupercapacitors (MSCs) are printed on textile and paper substrates by optimizing the nozzle geometry for high‐resolution inkjet printing. The chemical stability and electrical properties of the printed devices are also studied after storing the devices for six months under ambient conditions. Current collector‐free, textile‐based MSCs show areal capacitance values up to 294 mF cm −2 (2 mV s −1 ) in poly(vinyl alcohol)/sulfuric acid gel electrolyte, surpassing reported printed MXene‐based MSCs and inkjet‐printed MSCs using other 2D nanomaterials. This work is an important step toward increasing the functional capacity of conductive inks and simplifying the fabrication of wearable textile‐based electronics.
Uzun, Simge↗
Activating Layered Metal Oxide Nanomaterials via Structural Engineering as Biodegradable Nanoagents for Photothermal Cancer Therapy
Layered metal oxides including MoO 3 and WO 3 have been widely explored for biological applications owing to their excellent biocompatibility, low toxicity, and easy preparation. However, they normally exhibit weak or negligible near-infrared (NIR) absorption and thus are inefficient for photo-induced biomedical applications. Herein, the structural engineering of layered MoO 3 and WO 3 nanostructures is first reported to activate their NIR-II absorption for efficient photothermal cancer therapy in the NIR-II window. White-colored micrometre-long MoO 3 nanobelts are transformed into blue-colored short, thin, defective, interlayer gap-expanded MoO 3–x nanobelts with a strong NIR-II absorption via the simple lithium treatment. The blue MoO 3–x nanobelts exhibit a large extinction coefficient of 18.2 L g –1 cm –1 and high photothermal conversion efficiency of 46.9% at 1064 nm. After surface modification, the MoO 3–x nanobelts can be used as a robust nanoagent for photoacoustic imaging-guided photothermal therapy to achieve efficient cancer cell ablation and tumor eradication under irradiation by a 1064 nm laser. Importantly, the biodegradable MoO 3–x nanobelts can be rapidly degraded and excreted from body. We report the study highlights that the structural engineering of layered metal oxides is a powerful strategy to tune their properties and thus boost their performances in given applications.
36 MATERIALS SCIENCE↗
Bifunctional Ionic Covalent Organic Networks for Enhanced Simultaneous Removal of Chromium(VI) and Arsenic(V) Oxoanions via Synergetic Ion Exchange and Redox Process
Chromium (VI) and arsenic (V) oxoanions are major toxic heavy metal pollutants in water threatening both human health and environmental safety. Here, the development is reported of a bifunctional ionic covalent organic network (iCON) with integrated guanidinium and phenol units to simultaneously sequester chromate and arsenate in water via a synergistic ion-exchange-redox process. The guanidinium groups facilitate the ion-exchange-based adsorption of chromate and arsenate at neutral pH with fast kinetics and high uptake capacity, whereas the integrated phenol motifs mediate the Cr(VI)/Cr(III) redox process that immobilizes chromate and promotes the adsorption of arsenate via the formation of Cr(III)-As(V) cluster/complex. The synergistic ion-exchange-redox approach not only pushes high adsorption efficiency for both chromate and arsenate but also upholds a balanced Cr/As uptake ratio regardless of the change in concentration and the presence of interfering oxoanions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mycosynthesis of Zinc Oxide Nanoparticles Exhibits Fungal Species Dependent Morphological Preference
Filamentous fungi can synthesize a variety of nanoparticles (NPs), a process referred to as mycosynthesis that requires little energy input, do not require the use of harsh chemicals, occurs at near neutral pH, and do not produce toxic byproducts. While NP synthesis involves reactions between metal ions and exudates produced by the fungi, the chemical and biochemical parameters underlying this process remain poorly understood. Here, the role of fungal species and precursor salt on the mycosynthesis of zinc oxide (ZnO) NPs is investigated. This data demonstrates that all five fungal species tested are able to produce ZnO structures that can be morphologically classified into i) well-defined NPs, ii) coalesced/dissolving NPs, and iii) micron-sized square plates. Further, species-dependent preferences for these morphologies are observed, suggesting potential differences in the profile or concentration of the biochemical constituents in their individual exudates. This data also demonstrates that mycosynthesis of ZnO NPs is independent of the anion species, with nitrate, sulfate, and chloride showing no effect on NP production. Finally, these results enhance the understanding of factors controlling the mycosynthesis of ceramic NPs, supporting future studies that can enable control over the physical and chemical properties of NPs formed through this “green” synthesis method.
59 BASIC BIOLOGICAL SCIENCES↗
Reversible Iron Oxyfluoride (FeOF)–Graphene Composites as Sustainable Cathodes for High Energy Density Lithium Batteries
Two large barriers are impeding the wide implementation of electric vehicles, namely driving-range and cost, primarily due to the low specific energy and high cost of mono-valence cathodes used in lithium-ion batteries. Iron is the ideal element for cathode materials considering its abundance, low cost and toxicity. However, the poor reversibility of (de)lithiation and low electronic conductivity prevent iron-based high specific energy multi-valence conversion cathodes from practical applications. In this work, a sustainable FeOF nanocomposite is developed with extraordinary performance. The specific capacity and energy reach 621 mAh g –1 and 1124 Wh kg –1 with more than 100 cycles, which triples the specific capacity, and doubles the specific energy of current mono-valence intercalation LiCoO 2 . This is the result of an effective approach, combing the nanostructured FeOF with graphene, realized by making the (de)lithiation reversible by immobilizing FeOF nanoparticles and the discharge products over the graphene surface and providing the interparticle electric conduction. Importantly, it demonstrates that introducing small amount of graphene can create new materials with desired properties, opening a new avenue for altering the (de)lithiation process. Finally, such extraordinary performance represents a significant breakthrough in developing sustainable conversion materials, eventually overcoming the driving range and cost barriers.
25 ENERGY STORAGE↗
Redox Chemical‐Fueled Dissipative Self‐Assembly of Active Materials
Abstract This work reports a new transient self‐assembly of active materials fueled solely by a mild redox reaction network. Fuel‐driven dissipative, out‐of‐equilibrium assemblies are common in living systems but are challenging to mimic synthetically. Synthetic dissipative assembly systems developed thus far often use relatively toxic fuels and harsh conditions. Herein we report a transient, out‐of‐equilibrium self‐assembly system based on a new chemical reaction network using redox reactions. We use a mild redox chemical reaction network to simultaneously create and destroy a disulfide‐based hydrogelator, leading to transient, dynamic behavior. By closely regulating the reaction kinetics and reagent composition, the macroscopic properties of the active materials are fine‐tuned. The current work represents an important step toward the development of active materials operating under mild conditions.
Ogden, William A.↗
An Emerging Trend in the Synthesis of Iron Titanate Photocatalyst Toward Water Splitting
Hydrogen gas is a prominent focus in pursuing renewable and clean alternative energy sources. The quest for maximizing hydrogen production yield involves the exploration of an ideal photocatalyst and the development of a simple, cost-effective technique for its generation. Iron titanate has garnered attention in this context due to its photocatalytic properties, affordability, and non-toxic nature. Over the years, different synthesis routes, different morphologies, and some modifications of iron titanate have been carried out to improve its photocatalytic performance by enhancing light absorption in the visible region, boosting charge carrier transfer, and decreasing recombination of electrons and holes. The use of iron titanate photocatalyst for hydrogen evolution reaction has seen an upward trend in recent times, and based on available findings, more can be done to improve the performance. This review paper provides a comprehensive overview of the fundamental principles of photocatalysis for hydrogen generation, encompassing the synthesis, morphology, and application of iron titanate-based photocatalysts. The discussion delves into the limitations of current methodologies and present and future perspectives for advancing iron titanate photocatalysts. By addressing these limitations and contemplating future directions, the aim is to enhance the properties of materials fabricated for photocatalytic water splitting.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Algebraic expressions for estimating the impact depths of a surface barrier over a homogeneous soil
Engineered surface barriers are used to isolate subsurface contaminants for effective long-term containment of municipal solid waste, other nonhazardous solid and liquid waste, hazardous and toxic wastes, and radioactive waste. The impact depths of a surface barrier are affected by the pre-barrier recharge rate and the properties of the soil beneath the barrier. In this paper, the pore-size-specific (PSS) water velocity is defined and an algebraic expression of PSS velocity is derived based on the stream tube concept and the Brooks and Corey hydraulic retention model. Algebraic expressions are developed to estimate drainage velocities and barrier impact depths after the emplacement of a surface barrier. Four impact depth terms are used to convey the protective effect: drainage front, average drainage, the location with 50% impact, and drainage tail. The drainage front depth is the deepest point at which the barrier has a detectable impact at a specific time (also called the near zero-impact depth). The average-impact depth is the depth at which average drainage occurs. At the 50% impact depth, the water flux rate is reduced by half because of the surface barrier. Lastly, the drainage tail depth (also called the full-impact depth) is the deepest depth at which the water conditions above it are in equilibrium with the barrier. The algebraic expressions show that the average-impact depth is no more than 1/3 of near zero-impact depth, while the 50% impact depth is slightly larger than 1/2 of the near zero-impact depth. The full-impact depth, depending on the final recharge rate from the surface barrier, is usually much smaller than the other impact depths. These differences lead to a very large transition zone beneath a surface barrier. Numerical simulations were conducted to replicate the same conditions. The numerical results corroborated the analytical models by predicting very similar water content profiles and near zero-, average-, 50%, and full-impact depths. The algebraic expressions provided in this paper are useful for quickly identifying sites where the depth of the existing contaminants could be beyond the protection of a surface barrier.
54 ENVIRONMENTAL SCIENCES↗
Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.
Structures provide a critical breakthrough step for biological analyses, and small angle X-ray scattering (SAXS) is a powerful structural technique to study dynamic DNA repair proteins. As toxic and mutagenic repair intermediates need to be prevented from inadvertently harming the cell, DNA repair proteins often chaperone these intermediates through dynamic conformations, coordinated assemblies, and allosteric regulation. By measuring structural conformations in solution for both proteins, DNA, RNA, and their complexes, SAXS provides insight into initial DNA damage recognition, mechanisms for validation of their substrate, and pathway regulation. Here, we describe exemplary SAXS analyses of a DNA damage response protein spanning from what can be derived directly from the data to obtaining super resolution through the use of SAXS selection of atomic models. We outline strategies and tactics for practical SAXS data collection and analysis. Making these structural experiments in reach of any basic and clinical researchers who have protein, SAXS data can readily be collected at government-funded synchrotrons, typically at no cost for academic researchers. In addition to discussing how SAXS complements and enhances cryo-electron microscopy, X-ray crystallography, NMR, and computational modeling, we furthermore discuss taking advantage of recent advances in protein structure prediction in combination with SAXS analysis.
Chinnam, Naga Babu↗
Horizontal gene transfer in Fungi
Horizontal gene transfer (HGT), the sharing of genes between species outside of inheritance, is a common feature among prokaryotes, but a growing body of evidence supports HGT in eukaryotic genomes. The driving forces behind horizontal gene transfer occur within a shared environment, and are selective—meaning they improve survivability of stress, increase nutrient access, or provide an evolutionary advantage. The development of toxic and pathogenic properties was one of the first indications of phenotypic transfer among fungal species. An growing species diversity of genome sequences has brought a new set of tools to tracking HGT. The detection of HGT based on sequence similarity utilizes species tree phylogenies, which compare similarity of core conserved genes to determine lineage. Divergence of an HGT candidate gene from a phylogenetic background tree can show inter-species DNA transfer. It is by following phenotypes and analysis of DNA sequence context and content that we can uncover previous transfer events, and track lab fostered and recorded HGT. Evidence of HGT is found heavily in parasitic and pathogenic fungi; both of these lifestyles rely on phagocytosis and assimilation of host parts and pieces, suggesting phagocytosis is implicated in DNA uptake mechanisms. Our understanding of the molecular mechanisms of DNA uptake and incorporation of foreign DNA into fungal genomes, i.e. natural competence, remain based on a set of laboratory conditions used in molecular transformation. The mechanism of DNA uptake in the natural world and new DNA incorporation remain under investigation.
Bredeweg, Erin L.↗
Diversity in Photoprotection and Energy Balancing in Terrestrial and Aquatic Phototrophs
The evolution of oxygenic photosynthesis enabled organisms to use sunlight as an energy source, allowing them to colonize new niches. At the same time, life (as we know it) places severe constraints on photosynthesis. For example, the initial reactions of photosynthesis involve highly energetic intermediates that, if not controlled, can generate highly toxic side products (especially reactive oxygen species, ROS), that can damage other essential components of the organisms it powers. Photosynthesis must therefore be tightly regulated to balance the need for efficient energy conversion with the necessity of avoiding photodamage (Gust D, Kramer D, Moore A, Moore T, Vermaas W, Mater Res Bull 33:383–389, 2008). A related constraint on photosynthesis is the need to precisely balance how much energy is stored in ATP and NADPH to precisely meet biochemical demands. If this balancing does not occur, the system will fail, leading to photodamage (Kramer DM, Evans JR, Plant Physiol 155:70–78, 2011). Consideration of these requirements is essential for efforts to improve the efficiency of photosynthesis by introducing CO 2 concentrating mechanisms, altering metabolism or biosynthetic pathways to shunt energy to alternative products (Kramer DM, Evans JR, Plant Physiol 155:70–78, 2011). These balancing processes must be extremely robust to contend with the rapid and unpredictable fluctuations in environmental conditions and metabolic demands that occur in nature. A large body of work has come from model systems, especially terrestrial higher plants and the green alga Chlamydomonas reinhardtii, leading to a model for the regulation of light reactions that involves 1) sensing of the pH gradient component of the thylakoid proton motive force (pmf), and 2) the redox state of the plastoquinone- and stromal pools. Over the short term, these sensors trigger regulation of light capture by altering the activity of ATP synthase leading to adjustments in lumen pH, which fine tunes light capture through nonphotochemical quenching (NPQ) and control of electron flow by adjusting the rate of PQH 2 oxidation at the b 6 f complex. Simultaneously, this system controls the balance of ATP/NADPH by adjusting electron flux to linear and cyclic electron flow pathways to balance ATP/NADPH. This integrated “pmf paradigm” model explains much of the existing data on plants and green algae, but may not extend to other diverse organisms. This review considers how advances in our understanding of photosynthesis over the past 7–8 years, particularly in the discoveries of diverse biochemical/biophysical mechanisms in aquatic photosynthetic species, affects the view of energy balance, including the shunting of electrons to O 2 through the flavodiiron proteins (FLV), the plastid terminal oxidase, the dissipation of electric field by ion movements, and the activation of alternative electron sinks. Furthermore, we will introduce the basic model that has been developed for higher plant chloroplasts, then contrast these with selected aquatic systems, focusing on how the differences impact the needs to re-balance both energy input and its partitioning into energy currencies.
Kanazawa, Atsuko↗
Magnesium Technology 2020
Magnesium and its alloys are being investigated widely for applications that require extraordinarily high strength-to-weight ratio, vibration damping, electromagnetic shielding, reduction in carbon footprint, sustainability improvements, and low toxicity. In the past decade or so, this drive has led to increased adoption of magnesium and its alloys in everyday products and it is no longer regarded as an esoteric material. The overarching goal of its widespread adoption and replacement of conventional materials such as steel and aluminum alloys has been restricted because of the cost of the material, limited sources of primary material, alloying constraints, high chemical reactivity, and challenges associated with its plasticity. Researchers, scientists, engineers, and economists from industry, government agencies and laboratories, and academic institutions alike are actively developing roadmaps for next-generation products and addressing these challenges as quickly as possible through unique and innovative methods. The TMS Magnesium Committee has been actively involved in providing a platform to these entities for disseminating the latest information, developments, and cutting-edge research and development, and showcasing the latest research and development trends related to magnesium and its alloys through the Magnesium Technology Symposium, which takes place every year at the TMS Annual Meeting. This proceedings volume retains the essence of this longstanding tradition. The twenty-first volume in the series, Magnesium Technology 2020, is the proceedings of the Magnesium Technology Symposium held during the 149th TMS Annual Meeting & Exhibition in San Diego, CA, February 23–27, 2020. The volume captures commentaries and papers from 15 different countries. The papers have been categorized systematically based on topics pertaining to magnesium production, casting and solidification, thermomechanical processing, deformation mechanisms, modeling, corrosion, and applications. The symposium began with keynote sessions that featured several distinguished invited speakers from government organizations and academia, who provided their perspectives on the state of the art, goals, and opportunities in magnesium alloy research and development. Dr. Carlos Tomé from Los Alamos National Laboratory, U.S. Department of Energy, discussed 3D characterization of mechanical twins across grain boundaries. This was followed by a talk on hierarchically structured ultrafine-grained magnesium alloys by Dr. Rajiv Mishra from the University of North Texas, USA, who presented an example of using friction stir additive manufacturing for implementing such microstructures at a component level. Dr. Mark Horstemeyer from Liberty University, USA, presented an overview of fatigue modeling to capture the corrosion-fatigue behavior of magnesium alloys. The final talk in this session was presented by Dr. Bin Jiang from Chongqing University, China, who presented a novel extrusion approach for achieving high-strength magnesium alloy plates.
Jordon, J. Brian↗