Latrunculin inhibits the microfilament-mediated processes during fertilization, cleavage and early development in sea urchins and mice
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Schatten, Gerald↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Evaluation of the Effect of Microalloying on Cleavage of Monocrystalline NiAl Using a Miniaturized Disk-Bend Test
It was originally proposed to investigate the effect of microalloying on the ductility of monocrystalline NiAl. The idea was to deposit selected elements on oriented crystals of NiAl using magnetron sputtering, followed by annealing at high temperatures to produce the doped specimens. The project was terminated before that stage of the research was reached, but useful results needed for that study were obtained during the lifetime of the program. Those results are described in this report.
Ardell, Alan J.↗
Evaluation of the Effect of Microalloying on Cleavage of Monocrystalline NiAl using a Miniaturized Disk-Bend Test
It was originally proposed to investigate the effect of microalloying on the ductility of monocrystalline NiAl. The idea was to deposit selected elements on oriented crystals of NiAl using magnetron sputtering, followed by annealing at high temperatures to produce the doped specimens. The project was terminated before that stage of the research was reached, but useful results needed for that study were obtained during the lifetime of the program. Those results are described in this resort.
Ardell, Alan J.↗
Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments
The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.
NASA Discipline Exobiology↗
Interfacial Active Sites for CO2 Assisted Selective Cleavage of C-C/C-H Bonds in Ethane
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99 GENERAL AND MISCELLANEOUS↗
Structural basis for RNA-guided DNA cleavage by IscB-ωRNA and mechanistic comparison with Cas9
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99 GENERAL AND MISCELLANEOUS↗
Investigating the impact of donor atoms of single-source precursors on f-element nanomaterial formation and mechanisms of initial bond cleavage
Nanotechnology is advancing exponentially, with novel discoveries and applications emerging every day across various fields, including environmental remediation, biomedicine, electronics, and textiles. Nanoparticles (NPs) are defined as particles with sizes ranging from 1 to 100 nm, and their properties are influenced by factors such as composition, phase, size, and shape. Single-source precursors (SSPs) offer a promising method for controlling the synthesis of phase-pure nanoparticles with the desired stoichiometry and have been successfully applied to prepare transition metal and lanthanide NPs. SSPs are molecular compounds that contain all the necessary components to form the final nanomaterial and decompose under mild conditions, such as heating, to create the solid-state product. The objective of this work was to garner a mechanistic understanding of cerium oxide NP formation from cerium SSPs. To achieve these goals, first, ligands with oxygen and sulfur donor atoms were synthesized; among the array of ligands synthesized, some were novel. These ligands were then chelated to cerium ions to synthesize cerium precursors. Initially, known cerium alkoxide precursors were synthesized. Subsequently, these basic cerium complexes were further manipulated through acid-base protonolysis reactions to install a diverse set of ligands. Within this body of work, 10 novel cerium precursors were successfully synthesized. The ligands and the SSPs were analyzed using nuclear magnetic resonance (NMR) and thermogravimetric analysis coupled with differential scanning calorimetry (TGA-DSC). These SSPs were then introduced to a collision-induced dissociation mass spectrometer (CID-MS), and their dissociation pathways were studied.
37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗
Catalytic consequences of hydrogen addition events and solvent-adsorbate interactions during guaiacol-H 2 reactions at the H 2 O-Ru(0 0 0 1) interface
Catalytic reactions of biomass-derived phenolics and H 2 occur on transition metal surfaces via competitive C–O cleavage and ring saturation pathways, with both requiring multiple hydrogen addition events before forming their respective rate limiting transition states. These events are markedly affected by solvent chemical identity, with polar protic solvents ionizing hydrogen adatoms (H*) to interfacial protons (H + ) and opening up new catalytic routes. Here, we establish the reaction coordinate space for guaiacol-H 2 reactions on Ru(0 0 0 1) using density functional theory and describe the atomic-scale effect of a polar protic solvent, H 2 O. Coupled H + and H* attack leads to quasi-equilibrated enol and keto intermediates as the precursors for C–O cleavage and ring saturation, respectively. For C–O cleavage, H 2 O solvent enables a lower energy pathway via concomitant transfer of the hydroxyl H + to the methoxy oxygen during C–OCH 3 cleavage, forming a charge separated [Ru(s)–(C 6 H 5 O – )…(H + )…OCH 3 ] transition state and reducing the barrier by up to 0.8 eV as compared to unassisted C–OCH 3 cleavage. For ring saturation, H* attack onto an unsaturated meta carbon is rate limiting with no direct solvent participation, suggesting that protic polar solvents selectively promote the C–O cleavage pathway. Taken together, we show that activating guaiacol for either C–O bond cleavage or ring saturation product formation depends on the reactive hydrogen identity (H* or H + ), enol/keto isomerization equilibrium, and accessibility of the proton assisted Car–OCH 3 cleavage transition state. Here, all such factors are tunable via changes to the solvent or metal identity.
09 BIOMASS FUELS↗
Data Analytics for Catalysis Predictions: Are We Ready Yet?
Catalysis informatics has received tremendous attention in recent years as a tool to design catalysts and discover unique descriptors that capture the relationships between chemical properties and catalytic performance. One of the stop-gaps in understanding catalytic effects, which is often ignored and limits the deployment of data science tools, relates to the lack of uniform data. The catalytic cleavage of C–X (X= H, C, N, and O) bonds is relevant to many fundamental catalytic processes. In this Perspective, we performed data analytics on four groups of C–X cleavage reactions that are common in production, upcycling, or reactive separation: the C–C cleavage in cyclopropyl alcohol, the C–H cleavage in hydroacylation reactions, the C–O cleavage in β-O-4 linkages, and the C–N cleavage in amides, using experimental data collected from the literature to understand their underlying correlations. Experimental variables of high impact are identified for each reaction by dimensionality reduction methods. We highlight the urgent need for experimental data sets that include full details on the reaction conditions, such as reagent concentration, reaction temperature, or time in machine-readable forms. We discuss the potential improvement of the data of these reactions and promising approaches such as autonomous experiments to fill the gaps in unbiased experimental data. Finally, we also address the early stage consideration of separation aspects in the experimental design of efficient catalytic systems for these fundamental examples of chemical reactivity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Emergence of catalytic function in prebiotic information-coding polymers
Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.
59 BASIC BIOLOGICAL SCIENCES↗
Emergence of catalytic function in prebiotic information-coding polymers
Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.
Tkachenko, Alexei V. (ORCID:000000031291243X)↗
Identification of surface-exposed domains on the reducing side of photosystem I
Photosystem I (PSI) is a multisubunit enzyme that catalyzes the light-driven oxidation of plastocyanin or cytochrome c6 and the concomitant photoreduction of ferredoxin or flavodoxin. To identify the surface-exposed domains in PSI of the cyanobacterium Synechocystis sp. PCC 6803, we mapped the regions in PsaE, PsaD, and PsaF that are accessible to proteases and N-hydroxysuccinimidobiotin (NHS-biotin). Upon exposure of PSI complexes to a low concentration of endoproteinase glutamic acid (Glu)-C, PsaE was cleaved to 7.1- and 6.6-kD N-terminal fragments without significant cleavage of other subunits. Glu63 and Glu67, located near the C terminus of PsaE, were the most likely cleavage sites. At higher protease concentrations, the PsaE fragments were further cleaved and an N-terminal 9.8-kD PsaD fragment accumulated, demonstrating the accessibility of Glu residue(s) in the C-terminal domain of PsaD to the protease. Besides these major, primary cleavage products, several secondary cleavage sites on PsaD, PsaE, and PsaF were also identified. PsaF resisted proteolysis when PsaD and PsaE were intact. Glu88 and Glu124 of PsaF became susceptible to endoproteinase Glu-C upon extensive cleavage of PsaD and PsaE. Modification of PSI proteins with NHS-biotin and subsequent cleavage by endoproteinase Glu-C or thermolysin showed that the intact PsaE and PsaD, but not their major degradation products lacking C-terminal domains, were heavily biotinylated. Therefore, lysine-74 at the C terminus of PsaE was accessible for biotinylation. Similarly, lysine-107, or lysine-118, or both in PsaD could be modified by NHS-biotin.
Non-NASA Center↗
Mechanistic insights to drive catalytic hydrogenation of formamide intermediates to methanol via deaminative hydrogenation
Amine-promoted hydrogenation of CO 2 to methanol typically proceeds via a formamide intermediate when amines are used as additives or if the hydrogenation is performed in carbon capture solvents. The catalysts used for the hydrogenation of the formamide intermediate dictate the selectivity of the products formed: 1) Deoxygenative hydrogenation (C–O bond cleavage) resulting in N-methylation of amine and deactivation of the solvent, 2) Deaminative hydrogenation (C–N bond cleavage) resulting in formation of methanol and regeneration of the solvent. To date, catalytic reductions of CO 2 with amine promoters suffer from poor selectively for methanol which we attribute to the limiting formamide intermediate, though to date, the conditions that favor C–N cleavage have yet to be fully understood. To better understand the reactivity of the formamide intermediates, a range of heterogenous catalysts were used to study the hydrogenation of formamide. Well-known gas phase CO 2 hydrogenation catalysts catalyze the hydrogenation of formamide to N-methyl product via C–O bond cleavage. However, the selectivity can be readily shifted to selective C–N bond cleavage by addition of an additive with sufficient basicity for both homogenous and heterogeneous catalytic systems. The base additive shifts the selectivity by deprotonating a hemiaminal intermediate formed in situ during the formamide hydrogenation. This prevents dehydration process leading to N-methylated product, which is a key capture solvent deactivation pathway that hinders amine use in carbon capture, utilization, and storage (CCUS). The findings from this study provide a roadmap on how to improve the selectivity of known heterogenous catalysts, enabling catalytic reduction of captured CO 2 to methanol.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors
A critical step for SARS-CoV-2 assembly and maturation involves the autoactivation of the main protease (MPro WT ) from precursor polyproteins. Upon expression, a model precursor of MPro WT mediates its own release at its termini rapidly to yield a mature dimer. A construct with an E290A mutation within MPro exhibits time dependent autoprocessing of the accumulated precursor at the N-terminal nsp4/nsp5 site followed by the C-terminal nsp5/nsp6 cleavage. In contrast, a precursor containing E290A and R298A mutations (MPro M ) displays cleavage only at the nsp4/nsp5 site to yield an intermediate monomeric product, which is cleaved at the nsp5/nsp6 site only by MPro WT . MPro M and the catalytic domain (MPro 1-199 ) fused to the truncated nsp4 region also show time-dependent conversion in vitro to produce MPro M and MPro 1-199 , respectively. The reactions follow first-order kinetics indicating that the nsp4/nsp5 cleavage occurs via an intramolecular mechanism. These results support a mechanism involving an N-terminal intramolecular cleavage leading to an increase in the dimer population and followed by an intermolecular cleavage at the C-terminus. Thus, targeting the predominantly monomeric MPro precursor for inhibition may lead to the identification of potent drugs for treatment.
59 BASIC BIOLOGICAL SCIENCES↗
Effect of hexylene glycol-altered microtubule distributions on cytokinesis and polar lobe formation in fertilized eggs of Ilyanassa obsoleta
Some effects of gravity on early morphogenesis are correlated with microtubule locations within cells. During first cleavage in Ilyanassa obsoleta embryos, a transitory polar lobe constriction forms and then relaxes, allowing the polar lobe to merge with one daughter cell. If the polar lobe is equally divided or removed, morphogenesis is severely disrupted. To examine microtuble locations during early Ilyanassa development, eggs were fixed and stained for polymerized alpha-tubulin during first cleavage. The mitotic apparatus assembles at the animal pole. The cleavage furrow forms between the asters, constricting to a stabilized intercellular bridge encircling midbody-bound microtubules, whereas the polar lobe constriction forms below and parallel to the spindle, constricting to a transitory intercellular bridge encircling no detectable microtubules. At metaphase an alpha-tubulin epitope is distributed throughout the spindle, whereas a beta-tubulin epitope is present predominantly in the asters. Incubation in hexylene glycol, a drug that increases microtubule polymerization, during mitosis causes the polar lobe constriction to tighten around polymerized alpha-tubulin and remain stably constricted. If hexylene glycol is removed, alpha-tubulin staining disappears from the polar lobe constriction, which relaxes, whereas microtubules remain in the cleavage furrow, which remains constricted. These observations suggest that asymmetric distribution of microtubules affects early Ilyanassa cleavage patterns, and that continued presence of microtubules extending through an intercellular bridge is important for stabilization of the bridge constriction prior to completion of cytokinesis. These data provide the basis for further analysis of the role of microtubules in possible microgravity disruptions of Ilyanassa development.
NASA Discipline Cell Biology↗
Differential localization of cytoplasmic myosin II isoforms A and B in avian interphase and dividing embryonic and immortalized cardiomyocytes and other cell types in vitro
Two principal isoforms of cytoplasmic myosin II, A and B (CMIIA and CMIIB), are present in different proportions in different tissues. Isoform-specific monoclonal and polyclonal antibodies to avian CMIIA and CMIIB reveal the cellular distributions of these isoforms in interphase and dividing embryonic avian cardiac, intestinal epithelial, spleen, and dorsal root ganglia cells in primary cell culture. Embryonic cardiomyocytes react with antibodies to CMIIB but not to CMIIA, localize CMIIB in stress-fiber-like-structures during interphase, and markedly concentrate CMIIB in networks in the cleavage furrow during cytokinesis. In contrast, cardiac fibroblasts localize both CMIIA and CMIIB in stress fibers and networks during interphase, and demonstrate slight and independently regulated concentration of CMIIA and CMIIB in networks in their cleavage furrows. V-myc-immortalized cardiomyocytes, an established cell line, have regained the ability to express CMIIA, as well as CMIIB, and localize both CMIIA and CMIIB in stress fibers and networks in interphase cells and in cleavage furrows in dividing cells. Conversely, some intestinal epithelial, spleen, and dorsal root ganglia interphase cells express only CMIIA, organized primarily in networks. Of these, intestinal epithelial cells express both CMIIA and CMIIB when they divide, whereas some dividing cells from both spleen and dorsal root ganglia express only CMIIA and concentrate it in their cleavage furrows. These results suggest that within a given tissue, different cell types express different isoforms of CMII, and that cells expressing either CMIIA or CMIIB alone, or simultaneously, can form a cleavage furrow and divide.
NASA Discipline Developmental Biology↗
Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes non-canonical oxidoreductases
White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic monomericcompounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into ß-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.
dioxygenase↗
Steric and Lewis Basicity Influence of the Second Coordination Sphere on Electrocatalytic CO 2 Reduction by Manganese Bipyridyl Complexes
This study aims to provide a greater insight into the balance between steric (bpy vs (Ph) 2 bpy vs mes 2 bpy ligands) and Lewis basic ((Ph) 2 bpy vs (MeOPh) 2 bpy vs (MeSPh) 2 bpy ligands) influence on the efficiencies of the protonation-first vs reduction-first CO 2 reduction mechanisms with [Mn I (R 2 bpy)(CO) 3 (CH 3 CN)] + precatalysts, and on their respective transition-state geometries/energies for rate-determining C–OH bond cleavage toward CO evolution. The presence of only modest steric bulk at the 6,6'-diphenyl-2,2'-bipyridyl ((Ph) 2 bpy) ligand has here allowed unique insight into the mechanism of catalyst activation and CO 2 binding by navigating a perfect medium between the nonsterically encumbered bpy-based and the highly sterically encumbered mes2bpy-based precatalysts. Cyclic voltammetry conducted in CO 2 -saturated electrolyte for the (Ph) 2 bpy-based precatalyst [2-CH 3 CN] + confirms that CO 2 binding occurs at the two-electron-reduced activated catalyst [2] – in the absence of an excess proton source, in contrast to prior assumptions that all manganese catalysts require a strong acid for CO 2 binding. This observation is supported by computed free energies of the parent–child reaction for [Mn–Mn] o dimer formation, where increased steric hindrance relative to the bpy-based precatalyst correlates with favorable CO 2 binding. A critical balance must be adhered to, however, as the absence of steric bulk in the bpy-based precatalyst [1-CH 3 CN] + maintains a lower overpotential than [2-CH 3 CN] + at the protonation-first pathway with comparable kinetic performance, whereas an ~2-fold greater TOF max is observed at its reduction-first pathway with an almost identical overpotential as [2-CH 3 CN] + . Notably, excessive steric bulk in the mes2bpy-based precatalyst [3-CH 3 CN] + results in increased activation free energies of the C–OH bond cleavage transition states for both the protonation-first and the reduction-first pathways relative to both [1-CH 3 CN] + and [2-CH 3 CN] + . In fact, [3-CH 3 CN] + requires a 1 V window beyond its onset potential to reach its peak catalytic current, which is in contrast to the narrower (<0.30 V) potential response window of the remaining catalysts here studied. Furthermore, voltammetry recorded under 1 atm of CO 2 with 2.8 M (5%) H 2 O establishes [2-CH 3 CN] + to have the lowest overpotential (η = 0.75 V) in the series here studied, attributed to its ability to lie “on the fence” when providing sufficient steric bulk to hinder (but not prevent) [Mn–Mn] o dimerization, while simultaneously having a limited steric impact on the free energy of activation for the rate-determining C–OH bond cleavage transition state. While the methoxyphenyl bpy-based precatalyst [4-CH 3 CN] + possesses an increased steric presence relative to [2-CH 3 CN] + , this is offset by its capacity to stabilize the C–OH bond cleavage transition states of both the protonation-first and the reduction-first pathways by facilitating second coordination sphere H-bonding stabilization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗