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At least 253 records · Page 14

Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)

The high morbidity and mortality associated with SARS-CoV-2 infection, the etiological agent of COVID-19, has had a major impact on global public health. Significant progress has been made in the development of an array of vaccines and biologics, however, the emergence of SARS-CoV-2 variants and breakthrough infections are an ongoing major concern. Furthermore, there is an existing paucity of small-molecule host and virus-directed therapeutics and prophylactics that can be used to counter the spread of SARS-CoV-2, and any emerging and re-emerging coronaviruses. Here, we describe herein our efforts to address this urgent need by focusing on the structure-guided design of potent broad-spectrum inhibitors of SARS-CoV-2 3C-like protease (3CL pro or Main protease), an enzyme essential for viral replication. The inhibitors exploit the directional effects associated with the presence of a gem-dimethyl group that allow the inhibitors to optimally interact with the S4 subsite of the enzyme. Several compounds were found to potently inhibit SARS-CoV-2 and MERS-CoV 3CL proteases in biochemical and cell-based assays. Specifically, the EC50 values of aldehyde 1c and its corresponding bisulfite adduct 1d against SARS-CoV-2 were found to be 12 and 10 nM, respectively, and their CC50 values were >50 μM. Furthermore, deuteration of these compounds yielded compounds 2c/2d with EC50 values 11 and 12 nM, respectively. Replacement of the aldehyde warhead with a nitrile (CN) or an α-ketoamide warhead or its corresponding bisulfite adduct yielded compounds 1g, 1e and 1f with EC50 values 60, 50 and 70 nM, respectively. High-resolution cocrystal structures have identified the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and, furthermore, have illuminated the mechanism of action of the inhibitors. Overall, the high Safety Index (SI) (SI=CC50/EC50) displayed by these compounds suggests that they are well-suited to conducting further preclinical studies.

3-Chymotrypsin-like protease (3CLpro)↗

Principle in developing novel fluorinated sulfone electrolyte for high voltage lithium-ion batteries

A new class of fluorinated sulfones, β-fluorinated sulfones, were designed and synthesized as electrolyte solvents for high voltage lithium-ion batteries. While the oxidation potential of β-fluorinated sulfones is slightly lower than that of α-fluorinated sulfones, it is still significantly higher than the oxidation potential of regular sulfones, which already possess fairly high anodic stability. However, β-fluorinated sulfones exhibit a significant decrease in reduction potential compared to α-fluorinated sulfones, rendering them more stable towards graphite anodes. Moreover, the reduced lithium solvating power of β-fluorinated sulfones compared to regular sulfones mitigates the transition metal dissolution of cathodes. Taken together, these middle ground properties of β-fluorinated sulfone-based electrolytes enable the very stable long-term cycling of graphite||LiNi 0.6 Co 0.2 Mn 0.2 O 2 full cells. Finally, the outstanding performance of β-fluorinated sulfones designed by applying the “golden middle way” paves a new path for the development of an effective electrolyte system.

25 ENERGY STORAGE↗

P-V-T equation of state of boron carbide

We report the P-V-T equation of state measurements of B 4 C to 50 GPa and approximately 2500 K in laser-heated diamond anvil cells. We obtain an ambient temperature, third-order Birch–Murnaghan fit to the P-V data that yields a bulk modulus K 0 of 221(2) GPa and derivative, (dK/dP) 0 of 3.3(1). These were used in fits with both a Mie–Grüneisen–Debye model and a temperature-dependent, Birch–Murnaghan equation of state that includes thermal pressure estimated by thermal expansion (α) and a temperature-dependent bulk modulus (dK 0 /dT). The ambient pressure thermal expansion coefficient (α 0 + α 1 T), Grüneisen γ(V) = γ 0 (V/V 0 ) q and volume-dependent Debye temperature, were used as input parameters for these fits and found to be sufficient to describe the data in the whole P-T range of this study.

36 MATERIALS SCIENCE↗

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗

A widespread family of molecular chaperones promotes the intracellular stability of type VIIb secretion system– exported toxins

To survive in highly competitive environments, bacteria use specialized secretion systems to deliver antibacterial toxins into neighboring cells, thereby inhibiting their growth. In many Gram-positive bacteria, the export of such toxins requires a membrane-bound molecular apparatus known as the type VIIb secretion system (T7SSb). Recently, it was shown that toxin recruitment to the T7SSb requires a physical interaction between a toxin and two or more so-called targeting factors, which harbor key residues required for T7SS-dependent protein export. However, in addition to these targeting factors, some toxins additionally require a protein belonging to the DUF4176 protein family. Here, by examining two toxin–DUF4176 protein pairs, we demonstrate that DUF4176 constitutes a family of toxin-specific molecular chaperones. In addition to being required for toxin stability in producing cells, we find that DUF4176 proteins facilitate toxin export by specifically interacting with a previously uncharacterized intrinsically disordered region found in many T7SS toxins. Using X-ray crystallography, we determine structures of several DUF4176 chaperones in their unbound state, and of a DUF4176 chaperone in complex with the binding site of its cognate toxin. These structures reveal that this binding site consists of a disordered amphipathic α-helix that requires interaction with its cognate chaperone for proper folding. Overall, we have identified a family of secretion system associated molecular chaperones found throughout T7SSb-containing Gram-positive bacteria.

Gkragkopoulou, Polyniki↗

Pathways to Electrochemical Ironmaking at Scale Via the Direct Reduction of Fe 2 O 3

Electrochemical ironmaking can provide an energy efficient, zero-emissions alternative to traditional methods of ironmaking, but the scalability of low-temperature electrochemical cells may be constrained by reactor throughput and the availability of acceptable feedstocks. Electrodes directly converting solid iron-oxide particles to metal circumvent traditional mass-transport limitations but are sensitive to both the particle size and nanoscale morphology of reactants. Furthermore, the effect of these properties on reactor throughput has not been systematically studied at model electrowinning surfaces. Here, we have used size-controlled, homologous α-Fe 2 O 3 particles to study how the nanoscale morphology of oxides influences the obtainable current density toward Fe metal and integrated these results in a technoeconomic model for alkaline iron electrowinning systems. Micron-scale α-Fe 2 O 3 with nanoscale porosity can be used to form Fe at current densities commensurate with industrial water electrolysis (>0.6 A cm –2 ) in the absence of external convection, providing a path to cost-competitive and scalable ironmaking using electrochemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

350 ps Ultrafast room-temperature scintillation realized on CsPbBr 3 -based single crystals via Br 2 over-doping

Ultrafast scintillators are essential for next-generation radiation detection, positron emission tomography, and high-speed medical imaging. All-inorganic CsPbBr 3 perovskites are attractive candidates because of their high stopping power, and excellent optical quality, yet their long carrier lifetimes result in slow scintillation responses on the order of hundreds of nanoseconds. Here, we demonstrate that controlled over-doping with Br 2 produces CsPbBr 3.03 single crystals with sub-nanosecond scintillation at room temperature while preserving crystal quality. Single crystals grown by the Bridgman method exhibit high transparency and maintain the orthorhombic perovskite structure. Br 2 over-doping induces a slight lattice expansion (about 0.42% increase in unit-cell volume) while maintaining the orthorhombic perovskite phase and high optical transparency. Optical absorption reveals a slight redshift of the absorption edge after Br 2 introduction, indicating a modified defect landscape. Time-resolved photoluminescence and radioluminescence measurements show that Br 2 doping creates dense and efficient recombination centers that reduce the scintillation decay time from more than 100 ns in undoped crystals to 350 ps under 5.486 MeV α-particle excitation, and the scintillation decay time decreases by two orders of magnitude. The doped crystals also achieve a spatial resolution of 12 lp mm −1 in X-ray imaging. These results reveal a defect-engineering route for achieving ultrafast scintillation in halide perovskites and highlight the potential of Br 2 -modified CsPbBr 3 for fast timing applications.

Li, Zongxiao [Chinese Academy of Sciences (CAS), N↗

Toward the Understanding of the Reaction Mechanism of Zn/MnO2 Batteries Using Non-alkaline Aqueous Electrolytes

Zn/MnO 2 systems using non-alkaline aqueous electrolytes have attracted tremendous interest as rechargeable aqueous Zn ion batteries due to their safety and high specific capacities. Despite their promising electrochemical performance, however, their reaction mechanism has remained elusive. Here in this paper, we examined the structural evolution of cryptomelane α-MnO 2 cathode by ex situ transmission electron microscopy after electrochemical testing using two different non-alkaline aqueous Zn electrolytes with acetate and triflate salts of different pH values. We have discovered that the systems tested in both electrolytes exhibit a dissolution–deposition reaction mechanism through dissolution–deposition of Mn 2+ ions from/on the cathodes with a display of similar discharge/charge product formation. We have also found that the cell tested using the acetate electrolyte shows evidence of structural irreversibility that might contribute to its rapid capacity degradation. This finding offers an important insight into optimizing the cathode design for enhanced electrochemical function of aqueous Zn/MnO 2 batteries.

25 ENERGY STORAGE↗

An atypical lipoteichoic acid from Clostridium perfringens elicits a broadly cross-reactive and protective immune response

Clostridium perfringens is a leading cause of food-poisoning and causes avian necrotic enteritis, posing a significant problem to both the poultry industry and human health. No effective vaccine against C. perfringens is currently available. Using an antiserum screen of mutants generated from a C. perfringens transposon-mutant library, here we identified an immunoreactive antigen that was lost in a putative glycosyltransferase mutant, suggesting that this antigen is likely a glycoconjugate. Following injection of formalin-fixed whole cells of C. perfringens HN13 (a laboratory strain) and JGS4143 (chicken isolate) intramuscularly into chickens, the HN13-derived antiserum was cross-reactive in immunoblots with all tested 32 field isolates, whereas only 5 of 32 isolates were recognized by JGS4143-derived antiserum. The immunoreactive antigens from both HN13 and JGS4143 were isolated, and structural analysis by MALDI-TOF-MS, GC-MS, and 2D NMR revealed that both were atypical lipoteichoic acids (LTAs) with poly-(β1→4)-ManNAc backbones substituted with phosphoethanolamine. However, although the ManNAc residues in JGS4143 LTA were phosphoethanolamine-modified, a few of these residues were instead modified with phosphoglycerol in the HN13 LTA. The JGS4143 LTA also had a terminal ribose and ManNAc instead of ManN in the core region, suggesting that these differences may contribute to the broadly cross-reactive response elicited by HN13. In a passive-protection chicken experiment, oral challenge with C. perfringens JGS4143 lead to 22% survival, whereas co-gavage with JGS4143 and α-HN13 antiserum resulted in 89% survival. This serum also induced bacterial killing in opsonophagocytosis assays, suggesting that HN13 LTA is an attractive target for future vaccine-development studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection

In the indeterminate nodules of a model legume Medicago truncatula, ~700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.

59 BASIC BIOLOGICAL SCIENCES↗

Shock compression of crystalline TeO 2 to the high-pressure fluid regime: Insights from ab initio molecular dynamics simulations

The shock response of fully-dense and porous crystalline tellurium dioxide (TeO 2 ⁠) to the high-pressure and high-temperature fluid regime was investigated within the framework of density functional theory with Mermin’s generalization to finite temperatures. The principal and porous shock Hugoniot curves were predicted from canonical ab initio molecular dynamics (AIMD) simulations, with the phase space sampled along isotherms up to 80 000 K, for densities ranging from ρ = 3 to 17 g/cm 3 . The polymorphs investigated are α-TeO 2 paratellurite (⁠P4 1 2 1 2), TeO 2 cotunnite (⁠Pnma⁠), and TeO 2 post-cotunnite (⁠P2 1 /m⁠). Based on the discontinuity found in the calculated U s – u p slope of TeO 2 post-cotunnite at a shock velocity of U s ≃ 8.35km/s and a particle velocity of u p ≃ 3.64 km/s, the shock melting temperature and pressure are predicted to be ≃ 6500 K and ≃ 170 GPa. Results from the AIMD simulations are in line with the static compression data of TeO 2 paratellurite and cotunnite, and with the recent shock Hugoniot data for single-crystal α- TeO 2 for pressures up to 85 GPa, obtained using the inclined-mirror method and the velocity interferometer system for any reflector combined with powder gun and two-stage light-gas gun.

74 ATOMIC AND MOLECULAR PHYSICS↗

Human α-defensin 5 suppressed colon cancer growth by targeting PI3K pathway

Defensins are highly conserved antimicrobial peptides, which ubiquitously expressed in different species. In addition to the functions in host defense, their aberrant expression have also been documented in cancerous tissue including breast cancer, lung caner and renal carcinoma etc. Whereas, roles of Defensin Alpha 5 (DEFA5) in colon cancer has not been explored. Bioinformatic analysis was used to study the expression of DEFA5 and its correlation with clinical outcomes; Western blot, qPCR, Co-immunoprecipitation, xenograft models were used to the study the molecular mechanism. Decreased expression of DEFA5 at protein level was observed in colon tissues. Colon cancer cell lines proliferation and colony formation capacity were significantly suppressed by DEFA5 overexpression. Moreover, in vivo tumor growth in nude mice was also suppressed by DEFA5 overexpression, suggesting a tumor suppressor role of DEFA5 in colon cancer. Mechanistically, DEFA5 directly binds to the subunits of PI3K complex, thus attenuates the downstream signaling transduction, leads to delayed cell growth and metastasis. Collectively, we concluded that DEFA5 showed an inhibitory effect in colon cancer cell growth and may serve as a potential tumor suppressor in colon cancer.

60 APPLIED LIFE SCIENCES↗

Impact of Stabilizing Cations on Lithium Intercalation in Tunneled Manganese Oxide Cathodes

Stabilizing cations such as K + , Ba 2+ , and Ag + are known to provide charge neutrality and enhance structural stability in low-cost tunneled manganese dioxide (MnO 2 ) cathodes for Li ion batteries. However, a fundamental understanding of the role of these cations in the electrochemical performance of tunneled MnO 2 cathodes remains unclear, especially at low stabilizing cation concentrations. Here, we employ density functional theory (DFT + U) calculations to reveal the impact of stabilizing potassium cation (K + ) concentration on the structural stability, electronic properties, and kinetics of lithium transport in 2 x 2 tunneled manganese oxide (α-K y Mn 8 O 16 , at y = 0, 1, and 2) battery cathodes during lithium intercalation. Specifically, we provide insights into the effect of K + ions on several critical factors governing the electrochemical storage performance of tunneled MnO2 cathodes, including (a) energetically favorable Li+ host sites, (ii) Li + and electron transport capabilities, (iii) optimal intercalation pathways, crystal distortion, microstructural stability, and tunneled-to-layer phase transformation as a function of lithium content, and (iv) cell output voltage profile. Interestingly, we find that low K + concentrations (y ≤ 1) yield partially cation-deficient tunnels in the MnO 2 cathode. Such unique tunnel structures in the cathode enable (a) low kinetic barriers for Li transport, (b) excellent thermodynamic stability of the tunneled structure even at a high Li + loading (up to ~ 0.625 Li/Mn), and (c) good electronic conductivity facilitated by Jahn-Teller distortions; all of which are critical for achieving high capacity batteries with enhanced rate capability. Additionally, these results provide perspectives to design low-cost transition metal oxide cathodes for high-performance Li-ion batteries with excellent cycle life.

25 ENERGY STORAGE↗

Heterotrimeric G‐protein, Gi1, is involved in the regulation of proliferation, neuronal migration, and dendrite morphology during cortical development in vivo

Abstract Heterotrimeric G‐proteins are composed of α, β, and γ subunits, and function as signal transducers. Critical roles of the α‐subunits of Gi/o family heterotrimeric G‐proteins, Gαi2, and Gαo1, have so far been reported in brain development and neurodevelopmental disorders. In this study, we tried to clarify the role of Gαi1, α‐subunit of another Gi/o family member Gi1, during corticogenesis, based on the recent identification of its gene abnormalities in neurodevelopmental disorders. In western blot analyses, Gαi1 was found to be expressed in mouse brain in a developmental stage‐dependent manner. Morphological analyses revealed that Gαi1 was broadly distributed in cerebral cortex with relatively high expression in the ventricular zone (VZ) at embryonic day (E) 14. Meanwhile, Gαi1 was enriched in membrane area of yet unidentified early mitotic cells in the VZ and the marginal zone at E14. Acute knockdown of Gαi1 with in utero electroporation in cerebral cortex caused cell cycle elongation of the neural progenitor cells and promoted their cell cycle exit. Gαi1‐deficient cortical neurons also exhibited delayed radial migration during corticogenesis, with abnormally elongated leading processes and hampered nucleokinesis. In addition, silencing of Gαi1 prevented basal dendrite development. The migration and dendritic phenotypes were at least partially rescued by an RNAi‐resistant version of Gαi1. Collectively, these results strongly suggest a crucial role of Gi1 in cortical development, and disturbance of its function may cause deficits in synaptic network formation, leading to neurodevelopmental disorders. image

Hamada, Nanako↗

Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography

The VP8* domain of spike protein VP4 in group A and C rotaviruses, which cause epidemic gastroenteritis in children, exhibits a conserved galectin-like fold for recognizing glycans during cell entry. In group B rotavirus, which causes significant diarrheal outbreaks in adults, the VP8* domain (VP8*B) surprisingly lacks sequence similarity with VP8* of group A or group C rotavirus. Here, by using the recently developed AlphaFold2 for ab initio structure prediction and validating the predicted model by determining a 1.3-Å crystal structure, we show that VP8*B exhibits a novel fold distinct from the galectin fold. This fold with a β-sheet clasping an α-helix represents a new fold for glycan recognition based on glycan array screening, which shows that VP8*B recognizes glycans containing N-acetyllactosamine moiety. Although uncommon, our study illustrates how evolution can incorporate structurally distinct folds with similar functionality in a homologous protein within the same virus genus.

59 BASIC BIOLOGICAL SCIENCES↗

Robust Synthetic Biology Toolkit to Advance Carboxysome Study and Redesign

Carboxysomes are polyhedral protein organelles that microorganisms use to facilitate carbon dioxide assimilation. They are composed of a modular protein shell that envelops an enzymatic core mainly composed of physically coupled Rubisco and carbonic anhydrase. While the modular construction principles of carboxysomes make them attractive targets as customizable metabolic platforms, their size and complexity can be a hindrance. In this work, we design and validate a plasmid set, the pXpressome toolkit, in which α-carboxysomes are robustly expressed and remain intact and functional after purification. We tested this toolkit by introducing mutations that influence carboxysome structure and performance. We find that deletion of vertex-capping genes results in formation of larger carboxysomes, while deletion of facet forming genes produces smaller particles, suggesting that adjusting the ratio of these proteins can rationally affect morphology. Through a series of fluorescently labeled constructs, we observe that this toolkit leads to more uniform expression and better cell health than previously published carboxysome expression systems. Overall, the pXpressome toolkit facilitates the study and redesign of carboxysomes with robust performance and improved phenotype uniformity. The pXpressome toolkit will support efforts to remodel carboxysomes for enhanced carbon fixation or serve as a platform for other nanoencapsulation goals.

59 BASIC BIOLOGICAL SCIENCES↗

p14 ARF forms meso-scale assemblies upon phase separation with NPM1

NPM1 is an abundant nucleolar chaperone that, in addition to facilitating ribosome biogenesis, contributes to nucleolar stress responses and tumor suppression through its regulation of the p14 Alternative Reading Frame tumor suppressor protein (p14 ARF ). Oncogenic stress induces p14 ARF to inhibit MDM2, stabilize p53 and arrest the cell cycle. Under non-stress conditions, NPM1 stabilizes p14 ARF in nucleoli, preventing its degradation and blocking p53 activation. However, the mechanisms underlying the regulation of p14 ARF by NPM1 are unclear because the structural features of the p14 ARF -NPM1 complex were elusive. Here we show that p14 ARF assembles into a gel-like meso-scale network upon phase separation with NPM1. This assembly is mediated by intermolecular contacts formed by hydrophobic residues in an α-helix and β-strands within a partially folded N-terminal portion of p14 ARF . These hydrophobic interactions promote phase separation with NPM1, enhance p14 ARF nucleolar partitioning, restrict NPM1 diffusion within condensates and nucleoli, and reduce cellular proliferation. Our structural analysis provides insights into the multifaceted chaperone function of NPM1 in nucleoli by mechanistically linking the nucleolar localization of p14 ARF to its partial folding and meso-scale assembly upon phase separation with NPM1.

59 BASIC BIOLOGICAL SCIENCES↗

Analysis of nickel sulfoselenide materials by XPS

Metal chalcogenides are of interest as electrocatalysts, battery materials, and more. XPS is a valuable tool for studying changes to these materials before and after catalysis, making reference spectra for the pristine materials valuable. Here, we present XPS spectra for a family of nickel sulfoselenide (NiSSe) materials based on the Ni 3 X 2 crystal structure, Ni 3 S 2-x Se x . XPS surveys and high-resolution spectra of Ni 2p, S 2p, S 2s, Se 3d, Se 3p, and Se 3s were recorded using Al K α radiation.

36 MATERIALS SCIENCE↗