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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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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Maximized lateral inhibition in paired magnetic domain wall racetracks for neuromorphic computing

Lateral inhibition is an important functionality in neuromorphic computing, modeled after the biological neuron behavior that a firing neuron deactivates its neighbors belonging to the same layer and prevents them from firing. In most neuromorphic hardware platforms lateral inhibition is implemented by external circuitry, thereby decreasing the energy efficiency and increasing the area overhead of such systems. Recently, the domain wall—magnetic tunnel junction (DW-MTJ) artificial neuron is demonstrated in modeling to be intrinsically inhibitory. Without peripheral circuitry, lateral inhibition in DW-MTJ neurons results from magnetostatic interaction between neighboring neuron cells. However, the lateral inhibition mechanism in DW-MTJ neurons has not been studied thoroughly, leading to weak inhibition only in very closely-spaced devices. This work approaches these problems by modeling current- and field- driven DW motion in a pair of adjacent DW-MTJ neurons. We maximize the magnitude of lateral inhibition by tuning the magnetic interaction between the neurons. The results are explained by current-driven DW velocity characteristics in response to an external magnetic field and quantified by an analytical model. Dependence of lateral inhibition strength on device parameters is also studied. Finally, lateral inhibition behavior in an array of 1000 DW-MTJ neurons is demonstrated. Our results provide a guideline for the optimization of lateral inhibition implementation in DW-MTJ neurons. Finally, with strong lateral inhibition achieved, a path towards competitive learning algorithms such as the winner-take-all are made possible on such neuromorphic devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Single-molecule tracking reveals dual front door/back door inhibition of Cel7A cellulase by its product cellobiose

Degrading cellulose is a key step in the processing of lignocellulosic biomass into bioethanol. Cellobiose, the disaccharide product of cellulose degradation, has been shown to inhibit cellulase activity, but the mechanisms underlying product inhibition are not clear. We combined single-molecule imaging and biochemical investigations with the goal of revealing the mechanism by which cellobiose inhibits the activity of Trichoderma reesei Cel7A, a well-characterized exo-cellulase. We find that cellobiose slows the processive velocity of Cel7A and shortens the distance moved per encounter; effects that can be explained by cellobiose binding to the product release site of the enzyme. Cellobiose also strongly inhibits the binding of Cel7A to immobilized cellulose, with a K i of 2.1 mM. The isolated catalytic domain (CD) of Cel7A was also inhibited to a similar degree by cellobiose, and binding of an isolated carbohydrate-binding module to cellulose was not inhibited by cellobiose, suggesting that cellobiose acts on the CD alone. Finally, cellopentaose inhibited Cel7A binding at micromolar concentrations without affecting the enzyme’s velocity of movement along cellulose. Together, these results suggest that cellobiose inhibits Cel7A activity both by binding to the “back door” product release site to slow activity and to the “front door” substrate-binding tunnel to inhibit interaction with cellulose. These findings point to strategies for engineering cellulases to reduce product inhibition and enhance cellulose degradation, supporting the growth of a sustainable bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Consequences of product inhibition in the quantification of kinetic parameters

While the potential for product inhibition in catalytic reactions is well known, the impact of neglected inhibition on measured kinetic parameters is often overlooked. The presence of product inhibition, most often caused by the competitive adsorption of products with reactants on catalytic active sites, is difficult to determine a priori for an arbitrary catalytic system. The significance of product inhibition relies on the concentration of the products, their adsorption thermodynamics on catalytically relevant sites, and process parameters such as temperature and pressure. When inhibition is significant, however, apparent activation energies and reaction orders vary from the differential-reactor apparent activation energy by a factor of 1/(1 - δ), where δ is the total inhibition order (e.g., the factor (1 - δ) = 1.6 for a system with product inhibition of -0.6 order). This is illustrated here with the kinetics of NO oxidation over Cu ion clusters (Cu x O y ) in Cu-SSZ-13, for which the product NO 2 inhibits the forward reaction. Furthermore, in the presence of inhibition, when only reactants are fed to a flow reactor or placed in a batch reactor, there is often no practical conversion that is low enough to guarantee differential behavior. Inclusion of products in the feed solves this problem, allowing accurate determination of kinetic parameters such as apparent reaction orders and activation energies. We also demonstrate that evaluation of the necessity of co-feeding products to assure measurement of differential-reactor data in a given catalytic system is straightforward from a plot of the log of the rate (or conversion) versus the log of the space time in a flow reactor or elapsed time in a batch reactor. We encourage inclusion of this test in all kinetic analyses that are reasonably approximated by power law rate expressions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

New insights into Mn 2+ and Mg 2+ inhibition of calcite growth

Impurity ion and isotope partitioning into carbonate minerals provide a window into the molecular processes occurring at the fluid-mineral interface during crystal growth. Here, we employ calcium isotope fractionation together with process-based modeling to elucidate the mechanisms by which two divalent cations with starkly contrasting compatibility, magnesium and manganese, inhibit calcite growth and incorporate into the mineral lattice. Calcite growth inhibition by Mg 2+ is log-linear and K Mg is on the order of 0.02–0.03 throughout the range of {Mg 2+ }/{Ca 2+ } studied here (0.01–2.6). Mn 2+ exhibits much stronger log-linear growth rate inhibition at low Mn 2+ concentrations (fluid {Mn 2+ }/{Ca 2+ } = 0.001–0.02). Mn 2+ is readily incorporated into the calcite lattice to form a calcite-rhodochrosite solid solution, with large partition coefficients (K Mn 4.6–15.6) inversely correlated to growth rate. For both Mn 2+ and Mg 2+ , calcium isotope fractionation is found to be invariant with {Me 2+ }/{Ca 2+ } despite more than an order of magnitude decline in growth rate. This invariant Δ 44/40 Ca suggests that the presence of Mn 2 + or Mg 2+ does not significantly change the relative rates of Ca 2+ attachment and detachment at kink sites during growth, indicative of a dominantly kink blocking inhibition mechanism. Because the partitioning behavior dictates that Mn 2+ must attach to the surface significantly faster than Ca 2+ , attachment of Mn 2+ is likely to be as a non-monomer species such as an ion pair or possibly a larger polynuclear cluster. We propose that calcite growth rate inhibition by Mn is determined by the kinetics of carbonate attachment at Mn-occupied kink sites, potentially due to slow re-orientation kinetics of carbonate ions that have formed an inner-sphere complex with Mn 2+ at the surface but must reorient to incorporate into the lattice. We demonstrate that patterns in Mg 2+ partitioning and inhibition behavior are broadly consistent with growth inhibition driven by slow Mg 2+ -aquo complex dehydration relative to Ca 2+ but argue that this mechanism likely represents one endmember scenario, seen in Mg-calcite growth at low supersaturations and net precipitation rates. During growth at faster net precipitation rates, some portion of Mg 2+ is likely incorporated as a partially hydrated or otherwise complexed species, but calcite growth remains significantly inhibited by the kinetics of CO 3 2- attachment at Mg 2+ kink sites. These findings suggest a hybrid classical/nonclassical growth mechanism whereby Ca 2+ incorporates largely as a free ion at kink sites while Mn 2+ and some portion of Mg 2+ are incorporated via non-monomer attachment. This pattern may be generalizable; trace constituent cations with aquo-complex desolvation rates significantly slower than the mineral growth rate preferentially incorporate as a non-monomer species during otherwise classical crystal growth.

58 GEOSCIENCES↗
DOE OSTI2021

Continuous NF-κB pathway inhibition promotes expansion of human phenotypical hematopoietic stem/progenitor cells through metabolism regulation

Highlights: • Small molecular inhibition of NF-κB pathway efficiently expands human HSPCs. • NF-κB inhibition with TPCA-1 improves the self-renewal potential and biological function maintenance of expanded CD34{sup +} cells. • NF-κB pathway inhibition reprograms metabolism and enhances glycolysis. • Continuous NF-κB inhibition is required in the culture process to facilitate primitive HSC maintenance. Hematopoietic stem/progenitor cells (HSPCs) ex vivo expansion is critical in facilitating their widespread clinical application. NF-κB pathway is implicated in the energy homeostasis and metabolic adaptation. To explore the effect of NF-κB pathway on the ex vivo HSPC expansion and metabolism, the 50 nM–1 μM inhibitor of NF-κB pathway TPCA-1 was used to expand cord blood derived CD34{sup +} cells in serum-free culture. The expansion folds, function, mitochondrial profile and metabolism of HSPCs were determined. After 10 days of culture with 100 nM TPCA-1, the expansion of total cells CD34{sup +}CD38{sup −} cells and CD34{sup +}CD38{sup −}CD45RA{sup −}CD90{sup +}CD49f{sup +} cells were significantly increased compared to the cytokine priming alone. Notably, TPCA-1 treatment generated ~ 2-fold greater percentage of CD34{sup +}EPCR{sup +} and CD34{sup +}CD38{sup −}CD45RA{sup −}CD90{sup +}CD49f{sup +} cells compared to cytokine only conditions. Moreover, TPCA-1 expanded CD34{sup +} cells displayed enhanced serial colonies forming potential and secondary expansion capability. NF-κB inhibition increased the expression of self-renewal related genes, while downregulated the expression of mitochondrial biogenesis regulator (Pgc1α) and mitochondrial chaperones and proteases (ClpP, Hsp10, Hsp60). Mitochondrial mass and membrane potential were markedly decreased with TPCA-1 treatment, leading to the reduced mitochondrial reactive oxygen species (ROS) level in HSPCs. NF-κB inhibition displayed augmented glycolysis rate with compromising mitochondrial metabolism. This study demonstrated that NF-κB pathway inhibition improved glycolysis and limited ROS production that promoted the ex vivo expansion and maintenance of functional HSPCs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Water-soluble saponins accumulate in drought-stressed switchgrass and may inhibit yeast growth during bioethanol production

Abstract Background Developing economically viable pathways to produce renewable energy has become an important research theme in recent years. Lignocellulosic biomass is a promising feedstock that can be converted into second-generation biofuels and bioproducts. Global warming has adversely affected climate change causing many environmental changes that have impacted earth surface temperature and rainfall patterns. Recent research has shown that environmental growth conditions altered the composition of drought-stressed switchgrass and directly influenced the extent of biomass conversion to fuels by completely inhibiting yeast growth during fermentation. Our goal in this project was to find a way to overcome the microbial inhibition and characterize specific compounds that led to this inhibition. Additionally, we also determined if these microbial inhibitors were plant-generated compounds, by-products of the pretreatment process, or a combination of both. Results Switchgrass harvested in drought (2012) and non-drought (2010) years were pretreated using Ammonia Fiber Expansion (AFEX). Untreated and AFEX processed samples were then extracted using solvents (i.e., water, ethanol, and ethyl acetate) to selectively remove potential inhibitory compounds and determine whether pretreatment affects the inhibition. High solids loading enzymatic hydrolysis was performed on all samples, followed by fermentation using engineered Saccharomyces cerevisiae . Fermentation rate, cell growth, sugar consumption, and ethanol production were used to evaluate fermentation performance. We found that water extraction of drought-year switchgrass before AFEX pretreatment reduced the inhibition of yeast fermentation. The extracts were analyzed using liquid chromatography–mass spectrometry (LC–MS) to detect compounds enriched in the extracted fractions. Saponins, a class of plant-generated triterpene or steroidal glycosides, were found to be significantly more abundant in the water extracts from drought-year (inhibitory) switchgrass. The inhibitory nature of the saponins in switchgrass hydrolysate was validated by spiking commercially available saponin standard (protodioscin) in non-inhibitory switchgrass hydrolysate harvested in normal year. Conclusions Adding a water extraction step prior to AFEX-pretreatment of drought-stressed switchgrass effectively overcame inhibition of yeast growth during bioethanol production. Saponins appear to be generated by the plant as a response to drought as they were significantly more abundant in the drought-stressed switchgrass water extracts and may contribute toward yeast inhibition in drought-stressed switchgrass hydrolysates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Reinforcement expectation in the honeybee ( Apis mellifera ): Can downshifts in reinforcement show conditioned inhibition?

When animals learn the association of a conditioned stimulus (CS) with an unconditioned stimulus (US), later presentation of the CS invokes a representation of the US. When the expected US fails to occur, theoretical accounts predict that conditioned inhibition can accrue to any other stimuli that are associated with this change in the US. Empirical work with mammals has confirmed the existence of conditioned inhibition. But the way it is manifested, the conditions that produce it, and determining whether it is the opposite of excitatory conditioning are important considerations. Invertebrates can make valuable contributions to this literature because of the well-established conditioning protocols and access to the central nervous system (CNS) for studying neural underpinnings of behavior. Nevertheless, although conditioned inhibition has been reported, it has yet to be thoroughly investigated in invertebrates. Here, we evaluate the role of the US in producing conditioned inhibition by using proboscis extension response conditioning of the honeybee (Apis mellifera). Specifically, using variations of a “feature-negative” experimental design, we use downshifts in US intensity relative to US intensity used during initial excitatory conditioning to show that an odorant in an odor–odor mixture can become a conditioned inhibitor. We argue that some alternative interpretations to conditioned inhibition are unlikely. However, we show variation across individuals in how strongly they show conditioned inhibition, with some individuals possibly revealing a different means of learning about changes in reinforcement. We discuss how the resolution of these differences is needed to fully understand whether and how conditioned inhibition is manifested in the honeybee, and whether it can be extended to investigate how it is encoded in the CNS. It is also important for extension to other insect models. In particular, work like this will be important as more is revealed of the complexity of the insect brain from connectome projects.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro

Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia, leading to inappropriate antibiotic treatment. The soil Bacillus subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides, while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2×GYE (GYE) and Columbia colistin and nalidixic acid with 5% sheep’s blood agar inhibited the growth of Coccidioides, but microbiota grown on chocolate agar did not. Partial depletion of the microbiota through antibiotic disk diffusion revealed diminished inhibition and comparable growth of Coccidioides to controls. To characterize the bacteria grown and identify potential candidates contributing to the inhibition of Coccidioides, 16S rRNA sequencing was performed on tracheal and intestinal agar cultures and murine lung extracts. We found that the host bacteria likely responsible for this inhibition primarily included Lactobacillus and Staphylococcus. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

TMEM2 binds to CSNK2A3 to inhibit HBV infection via activation of the JAK/STAT pathway

To investigate mechanisms that TMEM2 activation inhibits hepatitis B virus (HBV) infection in hepatocarcinoma (HCC) cells, co-immunoprecipitation (Co-IP) and mass spectrometry were used in screening interacting proteins for TMEM2. Levels of casein kinase 2 subunit α3 (CSNK2A3) in HCC cells were found to be inhibited or overexpressed using siRNAs and pcDNA3.1-CSNK2A3, respectively. Effect of CSNK2A3 expression on cell proliferation was analyzed using MTS, while its effect on HBV infection was measured using ddPCR and IHC. Western blotting and JAK inhibitor ruxolitinib were also used to determine whether TMEM2-regulated CSNK2A3 expression and HBV infection were affected by JAK-STAT signaling. Co-IP and mass spectrometry results showed that CSNK2A3 interacts with TMEM2. Moreover, overexpression of CSNK2A3 significantly inhibited cell proliferation, while inhibition of CSNK2A3 promoted proliferation of HCC cells. In addition, overexpression of CSNK2A3 was observed to significantly enhance HBV infection, while siRNA knockdown of CSNK2A3 inhibited HBV infection. Notably, effect of CSNK2A3 overexpression on HBV infection was suppressed by TMEM2 overexpression. Further mechanistic analyses have revealed that TMEM2 could antagonize the effects of CSNK2A3 on cell proliferation and HBV infection via JAK-STAT pathway activation. In conclusion, TMEM2 has been determined to bind to CSNK2A3 to inhibit HBV infection via activation of the JAK-STAT pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Simultaneous inhibition of ATM, ATR, and DNA-PK causes synergistic lethality

Here, in this paper, we report that simultaneous inhibition of the three primary DNA damage recognition PI3 kinase-like kinases (PIKKs) —ATM, ATR, and DNA-PK— induces severe combinatorial synthetic lethality in mammalian cells. Utilizing Chinese hamster cell lines CHO and V79 and their respective PIKK mutants, we evaluated effects of inhibiting these three kinases on cell viability, DNA damage response, and chromosomal integrity. Our results demonstrate that while single or dual kinase inhibition increased cytotoxicity, inhibition of all three PIKKs results in significantly higher synergistic lethality, chromosomal aberrations, and DNA double-strand break (DSB) induction as calculated by their synergy scores. These findings suggest that the overlapping redundancy of ATM, ATR, and DNA-PK functions is critical for cell survival, and their combined inhibition greatly disrupts DNA damage signaling and repair processes, leading to cell death. This study provides insights into the potential of multi-targeted DDR kinase inhibition as an effective anticancer strategy, necessitating further research to elucidate underlying mechanisms and therapeutic applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Concentration‐Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering

Abstract Enzyme‐based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis ( Is PETase) is capable of PET hydrolysis under mild conditions but suffers from concentration‐dependent inhibition. In this study, this inhibition is found to be dependent on incubation time, the solution conditions, and PET surface area. Furthermore, this inhibition is evident in other mesophilic PET‐degrading enzymes to varying degrees, independent of the level of PET depolymerization activity. The inhibition has no clear structural basis, but moderately thermostable Is PETase variants exhibit reduced inhibition, and the property is completely absent in the highly thermostable HotPETase, previously engineered by directed evolution, which simulations suggest results from reduced flexibility around the active site. This work highlights a limitation in applying natural mesophilic hydrolases for PET hydrolysis and reveals an unexpected positive outcome of engineering these enzymes for enhanced thermostability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Molecular Design of Functional Polymers for Silica Scale Inhibition

Silica polymerization, which involves the condensation reaction of silicic acid, is a fundamental process with wide-ranging implications in biological systems, material synthesis, and scale formation. The formation of a silica-based scale poses significant technological challenges to energy-efficient operations in various industrial processes, including heat exchangers and water treatment membranes. Despite the common strategy of applying functional polymers for inhibiting silica polymerization, the underlying mechanisms of inhibition remain elusive. In this study, we synthesized a series of nitrogen-containing polymers as silica inhibitors and elucidated the role of their molecular structures in stabilizing silicic acids. Polymers with both charged amine and uncharged amide groups in their backbones exhibit superior inhibition performance, retaining up to 430 ppm of reactive silica intact for 8 h under neutral pH conditions. In contrast, monomers of these amine/amide-containing polymers as well as polymers containing only amine or amide functionalities present insignificant inhibition. Molecular dynamics simulations reveal strong binding between the deprotonated silicic acid and a polymer when the amine groups in the polymer are protonated. Notably, an extended chain conformation of the polymer is crucial to prevent proximity between the interacting monomeric silica species, thereby facilitating effective silica inhibition. Furthermore, the hydrophobic nature of alkyl segments in polymer chains disrupts the hydration shell around the polymer, resulting in enhanced binding with ionized silicic acid precursors compared to monomers. Finally, our findings provide novel mechanistic insights into the stabilization of silicic acids with functional polymers, highlighting the molecular design principles of effective inhibitors for silica polymerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Site requirements for inhibition-free CO oxidation over silica-supported bimetallic PdCu alloys

Pd catalysts are highly active for CO oxidation but suffer from inhibition by NO at low temperatures (<150 °C). We posit that incorporation of Cu into the Pd catalyst will improve low-temperature CO oxidation activity and reduce inhibition from competitive adsorbers. To probe this hypothesis, a series of PdCu alloys with different Pd : Cu ratios were synthesized and tested in the temperature-programmed oxidation of CO in the presence and absence of NO. Incorporation of small amounts of Cu into Pd improves the reactivity, as well as the resistance to NO inhibition. Beyond this, Cu incorporation into the Pd has a detrimental effect on the activity for CO oxidation. Based on combined infrared and X-ray absorption spectroscopy studies, here we show that high activity and resistance to inhibition requires alloying of Pd and Cu and the formation of a diverse surface, while surface segregation of Cu results in poor activity and inhibition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase

Rifampicin (Rif) is a first-line therapeutic used to treat the infectious disease tuberculosis (TB), which is caused by the pathogen Mycobacterium tuberculosis (Mtb). The emergence of Rif-resistant (Rif R ) Mtb presents a need for new antibiotics. Rif targets the enzyme RNA polymerase (RNAP). Sorangicin A (Sor) is an unrelated inhibitor that binds in the Rif-binding pocket of RNAP. Sor inhibits a subset of Rif R RNAPs, including the most prevalent clinical Rif R RNAP substitution found in Mtb infected patients (S456>L of the β subunit). In this paper, we present structural and biochemical data demonstrating that Sor inhibits the wild-type Mtb RNAP by a similar mechanism as Rif: by preventing the translocation of very short RNAs. By contrast, Sor inhibits the RifR S456L enzyme at an earlier step, preventing the transition of a partially unwound promoter DNA intermediate to the fully opened DNA and blocking the template-strand DNA from reaching the active site in the RNAP catalytic center. By defining template-strand blocking as a mechanism for inhibition, we provide a mechanistic drug target in RNAP. Our finding that Sor inhibits the wild-type and mutant RNAPs through different mechanisms prompts future considerations for designing antibiotics against resistant targets. Also, we show that Sor has a better pharmacokinetic profile than Rif, making it a suitable starting molecule to design drugs to be used for the treatment of TB patients with comorbidities who require multiple medications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Coculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadings

Abstract Background The cellulolytic thermophile Clostridium thermocellum is an important biocatalyst due to its ability to solubilize lignocellulosic feedstocks without the need for pretreatment or exogenous enzyme addition. At low concentrations of substrate, C. thermocellum can solubilize corn fiber > 95% in 5 days, but solubilization declines markedly at substrate concentrations higher than 20 g/L. This differs for model cellulose like Avicel, on which the maximum solubilization rate increases in proportion to substrate concentration. The goal of this study was to examine fermentation at increasing corn fiber concentrations and investigate possible reasons for declining performance. Results The rate of growth of C. thermocellum on corn fiber, inferred from CipA scaffoldin levels measured by LC–MS/MS, showed very little increase with increasing solids loading. To test for inhibition, we evaluated the effects of spent broth on growth and cellulase activity. The liquids remaining after corn fiber fermentation were found to be strongly inhibitory to growth on cellobiose, a substrate that does not require cellulose hydrolysis. Additionally, the hydrolytic activity of C. thermocellum cellulase was also reduced to less-than half by adding spent broth. Noting that > 15 g/L hemicellulose oligosaccharides accumulated in the spent broth of a 40 g/L corn fiber fermentation, we tested the effect of various model carbohydrates on growth on cellobiose and Avicel. Some compounds like xylooligosaccharides caused a decline in cellulolytic activity and a reduction in the maximum solubilization rate on Avicel. However, there were no relevant model compounds that could replicate the strong inhibition by spent broth on C. thermocellum growth on cellobiose. Cocultures of C. thermocellum with hemicellulose-consuming partners— Herbinix spp. strain LL1355 and Thermoanaerobacterium thermosaccharolyticum —exhibited lower levels of unfermented hemicellulose hydrolysis products, a doubling of the maximum solubilization rate, and final solubilization increased from 67 to 93%. Conclusions This study documents inhibition of C. thermocellum with increasing corn fiber concentration and demonstrates inhibition of cellulase activity by xylooligosaccharides, but further work is needed to understand why growth on cellobiose was inhibited by corn fiber fermentation broth. Our results support the importance of hemicellulose-utilizing coculture partners to augment C. thermocellum in the fermentation of lignocellulosic feedstocks at high solids loading.

09 BIOMASS FUELS↗
DOE OSTI2021

Ser 71 Phosphorylation Inhibits Actin-Binding of Profilin-1 and Its Apoptosis-Sensitizing Activity

The essential actin-binding factor profilin-1 (Pfn1) is a non-classical tumor suppressor with the abilities toboth inhibit cellular proliferation and augment chemotherapy-induced apoptosis. Besides actin, Pfn1 interacts with proteins harboring the poly-L-proline (PLP) motifs. Our recent work demonstrated that both nuclear localization and PLP-binding are required for tumor growth inhibition by Pfn1, and this is at least partially due to Pfn1 association with the PLP-containing ENL protein in the Super Elongation Complex (SEC) and the transcriptional inhibition of pro-cancer genes. In this paper, by identifying a phosphorylation event of Pfn1 at Ser 71 capable of inhibiting its actin-binding and nuclear export, we provide in vitro and in vivo evidence that chemotherapy-induced apoptotic sensitization by Pfn1 requires its cytoplasmic localization and actin-binding. With regard to tumor growth inhibition byPfn1, our data indicate a requirement for dynamic actin association and dissociation rendered by reversible Ser 71 phosphorylation and dephosphorylation. Furthermore, genetic and pharmacological experiments showed that Ser 71 of Pfn1 can be phosphorylated by protein kinase A (PKA). Taken together, our data provide novel mechanistic insights into the multifaceted anticancer activities of Pfn1 and how they are spatially-defined in the cell and differentially regulated by ligand-binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes

Abstract Complement evasion is a hallmark of extracellular microbial pathogens such as Borrelia burgdorferi, the causative agent of Lyme disease. Lyme disease spirochetes express nearly a dozen outer surface lipoproteins that bind complement components and interfere with their native activities. Among these, BBK32 is unique in its selective inhibition of the classical pathway. BBK32 blocks activation of this pathway by selectively binding and inhibiting the C1r serine protease of the first component of complement, C1. To understand the structural basis for BBK32-mediated C1r inhibition, we performed crystallography and size-exclusion chromatography–coupled small angle X-ray scattering experiments, which revealed a molecular model of BBK32-C in complex with activated human C1r. Structure-guided site-directed mutagenesis was combined with surface plasmon resonance binding experiments and assays of complement function to validate the predicted molecular interface. Analysis of the structures shows that BBK32 inhibits activated forms of C1r by occluding substrate interaction subsites (i.e., S1 and S1’) and reveals a surprising role for C1r B loop–interacting residues for full inhibitory activity of BBK32. The studies reported in this article provide for the first time (to our knowledge) a structural basis for classical pathway–specific inhibition by a human pathogen.

Garrigues, Ryan J. (ORCID:0000000259233250)↗
DOE OSTI2022

An auto-inhibited state of protein kinase G and implications for selective activation

Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here, we present a crystal structure of PKG Iβ in which the AI sequence and the cyclic nucleotide-binding (CNB) domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ AI sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I CNB domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wildtype cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.

59 BASIC BIOLOGICAL SCIENCES↗