Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “biochemicals”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

SPARC: Structural properties associated with residue constraints

SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ 54 , and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ 54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB ‘grabs’ ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

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)↗
DOE OSTI2025

Understanding the impacts of inorganic species in woody biomass for preprocessing and pyrolysis–A review

Woody biomass represents an abundant resource for sustainable biofuels, biochemicals, and bioproducts. Technologies for converting woody biomass have been established for decades, and research consistently highlights the critical role of inorganic species and ash plays in feedstock handling and conversion processes, including equipment plugging, corrosion, and catalyst deactivation. A thorough understanding of the variability, transport behavior, and downstream impact of inorganic species in woody biomass is essential for defining feedstock quality specifications and developing effective management strategies for conversion processes. This review compiles critical information in five main sections: 1) inorganic species concentration in woody biomass, based on anatomical fractions and their sources of variability; 2) technique features for quantifying inorganic elemental chemical analysis; 3) impacts of inorganic species on biomass preprocessing; 4) impacts of inorganic species on pyrolysis, and 5) mitigation strategies. Additionally, this review explores future challenges and opportunities in addressing the impacts of inorganic species on biomass quality. These insights aim to support the sustainable development of the biomass-to-bioenergy pipeline and ensure high-quality lignocellulosic feedstocks for efficient downstream conversions. The findings offer valuable guidance to policy makers, industry stakeholders, and researchers in developing effective strategies for managing inorganic species in woody biomass and fostering the sustainable processes for lignocellulosic biorefineries.

09 BIOMASS FUELS↗
DOE OSTI2023

Synchrotron-based X-ray fluorescence microscopy mapping the ionome of a toxic freshwater cyanobacterium

Harmful algal blooms (HABs) pose a major environmental concern across the globe. In abundance, cyanobacteria, or so-called green-blue algae can produce extremely dangerous cyanotoxins that harm humans and animals. This study focused on the mapping and distribution of intracellular macro-and micronutrients of the widespread freshwater cyanobacteria Microcystis aeruginosa (M. aeruginosa). Towards a better understanding of trace metal uptake and homeostasis throughout the cell cycle, we quantitatively mapped the spatial distribution of the elements P, K, Fe, Ca, Zn, Mn, and Cu across the ultrastructure of frozen-hydrated single cells using state-of-theart X-ray nanofluorescence imaging at the Advanced Photon Source (APS) at Argonne National Laboratory. Further, bulk cellular nutrient and trace metal content correlated well with the total intracellular elemental content in individual cells obtained by quantitative synchrotron X-ray fluorescence measurements. Multi-dimensional mappings showed P and K atoms colocalized as discrete semicircular hotspots that were analyzed with respect to their stoichiometry. Elevated Cu and Ca concentrations were detected along division plane of cells. P and K were found to have similar spatial elemental distribution with about 65% and 69% of the total cellular P and K, respectively, located at the hotspots. The P and K colocalization were refined further using nanotomography, showing a K envelope surrounding the P core. Inorganic P and organic P compounds were specified using solution-state 31 P nuclear magnetic resonance (NMR) spectroscopy from M. aeruginosa. Of the total extracted P determined by 31 P NMR spectroscopy, 47% were found to be nucleotides while only 11% were polyphosphates. Multimodal X-ray imaging provides a better understanding of intracellular biochemical processes in cyanobacteria, helping us monitor and combat an emerging environmental threat.

31P NMR spectroscopy↗
DOE OSTI2023

Understanding fundamental effects of biofuel structure on ignition and physical fuel properties

The development of biochemicals and biofuels with advantaged properties of higher combustion efficiency at lower emission levels can be aided by a priori prediction of critical global characteristics based on molecular structure. Existing predictive techniques are incomplete for comprehensive ignition and physical fuel property prediction. Here this investigation focuses on filling this knowledge gap by developing a priori prediction techniques for predicting important ignition as well as physical fuel properties of promising advantaged biofuels. We demonstrate the utility of this a priori prediction technique on saturated (≤C 5 ) alcohols, both linear and branched in nature by correlating their molecular structure with both important ignition and physical properties of the fuels. This work utilizes a semi-automated method of predicting ignition characteristics via accurate fundamental-based calculations of the fuel radical cascades that govern low-temperature combustion. This numerical methodology is supported by the relevant fuel ignition delay time (IDT) and research octane number (RON) data experimentally measured by the Advanced Fuel Ignition Delay Analyzer (AFIDA). Phyiscal fuel property trends are also analyzed by correlating the molecular structure of the fuel to its physical characteristics. Based on their molecular structure, recommendations are made on an a priori method for selecting biofuels that have advantaged properties for the selected fuel application. Lastly, the utility of this investigation is extended beyond the subset of alcohols considered by analyzing the IDT trends of i-Pentanol and n-Hexanol, revealing the fidelity of the novel kinetic modelling approach and the accuracy of the predicted trends in this study.

09 BIOMASS FUELS↗
DOE OSTI2020

Comparing first- and second-generation bioethanol by-products from sugarcane: Impact on soil carbon and nitrogen dynamics

The first- and second-generation bioethanol by-products (bagasse and fermentation by-product, respectively) have different biochemical characteristics relating to carbon (C) and nitrogen (N) due to their production processes. To examine the impacts of fermentation by-product and bagasse on soil C and N dynamics, a 120 day laboratory incubation experiment was conducted by applying these amendments in soil at an equal carbon application rate (2.2 g C kg -1 soil). There was a significant increase in overall cumulative CO 2 -C production from amended soil compared to the control soil, though the loss was greatest in bagasse amended soil. However, δ13C-CO 2 measurements suggested that fermentation by-product addition suppressed native soil C mineralization and prompted strong negative C priming (-57%). In contrast, bagasse amendment maintained similar native soil C mineralization to control soil. Decreased microbial biomass turnover time appears to be the major driving force for increased CO 2 -C production and soil C loss following bioethanol by-product amendments. Increased mineral N production indicated net N mineralization after fermentation by-product addition, while addition of bagasse resulted in lower N availability and N immobilization. Overall, results suggested that fermentation by-product application is advantageous in maintaining native soil C stock and N mineralization compared to bagasse. Thus, in a sustainable second-generation bioethanol production system, bagasse may be used for second-generation bioethanol production and the cogenerated by-product could be used as an amendment to improve soil C stock and N availability.

09 BIOMASS FUELS↗
DOE OSTI2023

Microscale spatiotemporal patterns of water, soil organic carbon, and enzymes in plant litter detritusphere

Understanding biophysical and biochemical processes in detritusphere is critical to quantifying and modeling plant residue decomposition dynamics and subsequent soil organic carbon (C) accrual. The objectives of the study were to explore (i) micro-environmental conditions within the detritusphere formed around decomposing corn and soybean leaves, and (ii) the relationships between moisture distribution, enzyme activity, and C dynamics during decomposition. We assessed spatial and temporal dynamics of moisture distribution using X-ray and neutron computed tomography, and activities of β-glucosidase and chitinase, two enzymes involved in soil C and N processing, using zymography. We used 13 C labeled residue to track residue contribution to atmospheric CO 2 and soil organic C. Moisture redistribution pattern varied depending on the residue type. While the water was immediately absorbed by the corn leaves and maintained afterward, switchgrass leaves absorbed water more slowly and created water-deficient zones within ~1mm from the residue. This initial moisture depletion led to lower chitinase activity and residue-derived CO 2 emissions in switchgrass. In contrast to chitinase, β-glucosidase activity was influenced by a combination of vegetation history and residue type, and it was higher when the origin of the residue matched the vegetation history of the soil. Pore size had an opposite impact on the studied enzymes, supporting the notion that contrasting soil pore architecture can stimulate activities of different enzymes through a selection of dominant enzyme producers. We concluded that the decomposition dynamics of plant residues is not only a simple function of residue chemistry, but rather a combined effect of the vegetation history, in part through its effect on microbial community composition, the plant residue chemical and likely physical characteristics, and the soil pore structure in the detritusphere. Together, they create temporally dynamic micro-environmental conditions influencing decomposition. Specifically, our study demonstrated that the initial micro-environment formulated in detritusphere can play an important role in enzyme activities and consequent C dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer

Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Preclinical characterization of Pan-NKG2D ligand-binding NKG2D receptor decoys

NKG2D and its ligands are critical regulators of protective immune responses controlling infections and cancer, defining a crucial immune signaling axis. Current therapeutic efforts targeting this axis almost exclusively aim at enhancing NKG2D-mediated effector functions. However, this axis can drive disease processes when dysregulated, in particular, driving stem-like cancer cell reprogramming and tumorigenesis through receptor/ligand self-stimulation on tumor cells. Despite complexities with its structure and biology, we developed multiple novel engineered proteins that functionally serve as axis-blocking NKG2D “decoys” and report biochemical, structural, in vitro , and in vivo evaluation of their functionality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Exploring the binding properties and activities of ancestral expansins

Bacterial expansins are non-lytic proteins capable of loosening cellulose networks, offering promising applications in agriculture, biotechnology, and material science. Their ability to disrupt noncovalent interactions in biopolymer matrices such as cellulose and chitin positions them as valuable tools for upgrading abundant natural materials. However, their industrial use remains limited due to their relatively low wall-loosening activity compared to plant expansins. To address this limitation, we applied Ancestral Sequence Resurrection (ASR) to reconstruct and characterize ancient variants of the Bacillus subtilis expansin BsEXLX1. ASR is a powerful evolutionary tool that enables the inference and synthesis of ancestral proteins, allowing researchers to explore functional traits that may have been lost over time. This approach not only provides insights into protein evolution but also facilitates the design of proteins with enhanced properties, such as improved substrate affinity or structural stability. In this study, we combined biochemical and biophysical assays to evaluate the activity and binding behavior of ancestral expansins. Our results reveal that ancestral variants exhibit increased cellulose affinity, reduced binding to acidic polysaccharides, and greater salt resistance. Furthermore, these traits enhance their wall-loosening activity and demonstrate the utility of ASR in engineering surface-active proteins for industrial applications, particularly in biomass processing and cellulose modification.

09 BIOMASS FUELS↗
DOE OSTI2021

Rational approach to drug discovery for human schistosomiasis

Human schistosomiasis is a debilitating, life-threatening disease affecting more than 229 million people in as many as 78 countries. There is only one drug of choice effective against all three major species of Schistosoma, praziquantel (PZQ). However, as with many monotherapies, evidence for resistance is emerging in the field and can be selected for in the laboratory. Previously used therapies include oxamniquine (OXA), but shortcomings such as drug resistance and affordability resulted in discontinuation. Employing a genetic, biochemical and molecular approach, a sulfotransferase (SULT-OR) was identified as responsible for OXA drug resistance. By crystallizing SmSULT- OR with OXA, the mode of action of OXA was determined. This information allowed a rational approach to novel drug design. Our team approach with schistosome biologists, medicinal chemists, structural biologists and geneticists has enabled us to develop and test novel drug derivatives of OXA to treat this disease. Using an iterative process for drug development, we have successfully identified derivatives that are effective against all three species of the parasite. One derivative CIDD-0149830 kills 100% of all three human schistosome species within 5 days. The goal is to generate a second therapeutic with a different mode of action that can be used in conjunction with praziquantel to overcome the ever-growing threat of resistance and improve efficacy. The ability and need to design, screen, and develop future, affordable therapeutics to treat human schistosomiasis is critical for successful control program outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Optimizing Treatment in Intermediate-Risk Prostate Cancer: Secondary Analysis of a Randomized Phase 3 Trial

To identify patients with intermediate-risk prostate cancer (IRPC) benefiting from de-escalation of androgen deprivation therapy (ADT) and/or dose escalated radiation therapy (DERT), we performed a secondary analysis of a phase 3 trial by measuring biochemical failure (BF), distant metastases, prostate cancer–specific mortality, overall survival (OS), and distant metastases-free survival (DMFS) rates according to prognostic intermediate risk factors (IRF).

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Development of an enzyme cocktail to bioconvert untapped starch in sweet sorghum processing by-products: Part II. Application and economic potential

Demand for bioethanol and other biochemicals produced from agricultural crops has increased. Sweet sorghum has been identified as a promising bioenergy crop as it can produce starch, sugar, and fibrous biomass. During processing, starch accumulates in the juice sediments and clarification mud. And, while currently not recovered, it can be made accessible for fermentation by enzymatic hydrolysis. The enzymatic hydrolysis of starch in sweet sorghum processing streams was investigated, followed by fermentation of the resulting glucose to ethanol. The juice sediment contained sufficient starch to increase fermentable sugars by 127%, allowing a final ethanol titer of 11.1 vol%. The economics for fermentation of only dissolved sugars (Scenario 1) versus dissolved sugars and hydrolyzed starch (Scenario 2) were compared using a technoeconomic model. Fixed capital cost was found to be similar for both scenarios. For a set harvest period, Scenario 2 could produce 20% more ethanol; however, if the distillation by-product was dried and marketed as animal feed, Scenario 1 was more cost effective. A plant producing 5.6–5.7 Mkg of fuel ethanol per year had a minimum selling price of $0.67/kg of ethanol with concurrent production of animal feed and zero cost sweet sorghum processing. Finally, even with these optimistic assumptions, the estimated production cost was higher than the current wholesale price of fuel ethanol.

09 BIOMASS FUELS↗
DOE OSTI2021

Implementation of dietary methionine restriction using casein after selective, oxidative deletion of methionine

Dietary methionine restriction (MR) is normally implemented using diets formulated from elemental amino acids (AA) that reduce methionine content to 0.17%. However, translational implementation of MR with elemental AA-based diets is intractable due to poor palatability. To solve this problem and restrict methionine using intact proteins, casein was subjected to mild oxidation to selectively reduce methionine. Diets were then formulated using oxidized casein, adding back methionine to produce a final concentration of 0.17%. The biological efficacy of dietary MR using the oxidized casein (Ox Cas) diet was compared with the standard elemental MR diet in terms of the behavioral, metabolic, endocrine, and transcriptional responses to the four diets. The Ox Cas MR diet faithfully reproduced the expected physiological, biochemical, and transcriptional responses in liver and inguinal white adipose tissue. Collectively, these findings demonstrate that dietary MR can be effectively implemented using casein after selective oxidative reduction of methionine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Lytic polysaccharide monooxygenase synergized with lignin-degrading enzymes for efficient lignin degradation

Even though the discovery of lytic polysaccharide monooxygenases (LPMOs) has fundamentally shifted our understanding of biomass degradation, most of the current studies focused on their roles in carbohydrate oxidation. However, no study demonstrated if LPMO could directly participate to the process of lignin degradation in lignin-degrading microbes. This study showed that LPMO could synergize with lignin-degrading enzymes for efficient lignin degradation in white-rot fungi. The transcriptomics analysis of fungi Irpex lacteus and Dichomitus squalens during their lignocellulosic biomass degradation processes surprisingly highlighted that LPMOs co-regulated with lignin-degrading enzymes, indicating their more versatile roles in the redox network. Biochemical analysis further confirmed that the purified LPMO from I. lacteus CD2 could use diverse electron donors to produce H 2 O 2 , drive Fenton reaction, and synergize with manganese peroxidase for lignin oxidation. The results thus indicated that LPMO might uniquely leverage the redox network toward dynamic and efficient degradation of different cell wall components.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on β-1,3 and β-1,4 glycosidic bonds

Glycoside hydrolases (GH) are involved in the degradation of a wide diversity of carbohydrates and present several biotechnological applications. Many GH families are composed of enzymes with a single well-defined specificity. In contrast, enzymes from the GH16 family can act on a range of different polysaccharides, including β-glucans and galactans. SCLam, a GH16 member derived from a soil metagenome, an endo-β-1,3(4)-glucanase (EC 3.2.1.6), can cleave both β-1,3 and β-1,4 glycosidic bonds in glucans, such as laminarin, barley β-glucan, and cello-oligosaccharides. A similar cleavage pattern was previously reported for other GH16 family members. However, the molecular mechanisms for this dual cleavage activity on (1,3)- and (1,4)-β-D-glycosidic bonds by laminarinases have not been elucidated. In this sense, we determined the X-ray structure of a presumably inactive form of SCLam co-crystallized with different oligosaccharides. The solved structures revealed general bound products that are formed due to residual activities of hydrolysis and transglycosylation. Biochemical and biophysical analyses and molecular dynamics simulations help to rationalize differences in activity towards different substrates. Our results depicted a bulky aromatic residue near the catalytic site critical to select the preferable configuration of glycosidic bonds in the binding cleft. Altogether, these data contribute to understanding the structural basis of recognition and hydrolysis of β-1,3 and β-1,4 glycosidic linkages of the laminarinase enzyme class, which is valuable for future studies on the GH16 family members and applications related to biomass conversion into feedstocks and bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota

Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of polysaccharide utilization loci (PULs), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic β(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), Bacteroides uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct β-glucans. Ligand complexes provide definitive insight into β(1,3)-glucan selectivity in the HGM, including structural features enabling dual β(1,3)-glucan/mixed-linkage β(1,3)/β(1,4)-glucan-binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the trimodular BtSGBP-B and BuSGBP-B revealed a tandem repeat of carbohydrate-binding module-like domains connected by long linkers. In contrast, BfSGBP-B comprises a bimodular architecture with a distinct β-barrel domain at the C terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.

59 BASIC BIOLOGICAL SCIENCES↗