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Results for “affine analysis”

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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Amine-functionalized metal-organic framework ZIF-8 toward colorimetric CO 2 sensing in indoor air environment

Carbon dioxide (CO 2 ) has been shown to contribute to human health consequences indoors, such as shortness of breath, nasal and optic irritation, dizziness, and nausea. Here in this work, we explore the potential of metal–organic frameworks (MOFs) as highly-porous, crystalline sorbents for sensitive colorimetric CO 2 detection. In particular, the zeolitic imidazolate framework (ZIF-8) is chosen as the sorptive material due to its chemical stability and tunable CO 2 affinity. The colorimetric gas sensor is developed in methanol with three components: (i) MOF ZIF-8 as a high surface area adsorbent; (ii) ethylenediamine (ED) as the CO 2 -affinitive basic function; and (iii) phenolsulfonpthalein (PSP) as the pH indicator. Colorimetric assays and ratiometric analysis confirm a colorimetric response to variable CO 2 concentrations of relevance to indoor air quality. The color response is attributed to a zwitterion mechanism whereby ED reacts with CO 2 to form a zwitterionic intermediate. This intermediate is then deprotonated by the pH indicator, shifting the pH and inducing a color change. Given its simple fabrication, rapid and obvious response, and stability in ambient environment, the ZIF-8-based colorimetric sensor provides a promising route for an improved indoor air quality monitoring.

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

Low-pressure methanol synthesis from CO 2 over metal-promoted Ni-Ga intermetallic catalysts

Ni-Ga and M-Ni-Ga (M = Au, Co, Cu) catalysts were evaluated for methanol synthesis from CO 2 at 10 bar and 200-270°C. The following trend in turnover frequency (TOF) for CO 2 hydrogenation was observed: AuNiGa > CuNiGa > NiGa > CoNiGa, where TOF increased with decreasing catalyst affinity for CO. The presence of a third metal was found to influence both the formation of the Ni-Ga intermetallic phase as well as the number of available sites for CO chemisorption. Phase formation, catalyst composition and stability were evaluated using therm ogravimetric analysis (TGA), X-ray diffraction (XRD), X-ray fluorescence (XRF), scanning transmission electron microscopy and energy dispersive X-ray spectroscopy (STEM-EDX). Au-Ni-Ga, which showed a nearly 4-fold improvement in TOF at 263°C and 10 bar compared to Ni-Ga, consisted of Ni 3 Ga particles decorated with Au, as evidenced by post catalysis characterization.

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

A ligand discovery toolbox for the WWE domain family of human E3 ligases

The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15 N-NMR-based binding affinity assays and 19 F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso -ADP-ribose ( iso -ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Phaseolus vulgaris SUT1.1 is a high affinity sucrose–proton co–transporter

Plant sucrose transporters are required for phloem loading, and therefore are essential for plant growth and development. In common beans (Phaseolus vulgaris) there are only two sucrose transporters functionally characterized. Through a previous RNA-seq study, we identified a putative sucrose transporter in common bean, which we hypothesize to function in import of sucrose into plant cells. In silico analysis revealed that PvSUT1.1 is a putative sucrose-proton co-transporter distinct from other characterized sucrose transporters in common bean indicating that this is a previously undescribed transporter protein in beans. Further analysis revealed that PvSUT1.1 shares high protein sequence homology to the phloem loader Arabidopsis SUC2; both have 12 transmembrane domains, a typical characteristic of plant sucrose transporters. Heterologous expression in yeast further showed PvSUT1.1 to be functional and it imported sucrose into yeast cells with a K m of 0.7 mM sucrose. Import of sucrose through PvSUT1.1 is also pH-dependent with highest uptake at pH 4.0, and activity is lost in the presence of the uncoupler carbonyl cyanide 3-chlorophenylhydrazone. Consistent with identification of PvSUT1.1 as a Type I transporter, PvSUT1.1 also transports esculin. Finally, PvSUT1.1 showed expression in multiple tissues and the protein was localized to the plasma membrane. The results show that PvSUT1.1 is a sucrose transporter that is probably involved in the uptake of sucrose into source and sink cells. The potential role of PvSUT1.1 in leaf phloem loading of sucrose in common beans and its importance in heat tolerance of reproductive tissues are further discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tailoring Hierarchical Structure and Rare Earth Affinity of Compositionally Identical Polymers via Sequence Control

Macromolecule sequence, structure, and function are inherently intertwined. While well-established relationships exist in proteins, they are more challenging to define for synthetic polymer nanoparticles due to their molecular weight, sequence, and conformational dispersities. Furthermore, to explore the impact of sequence on nanoparticle structure, we synthesized a set of 16 compositionally identical, sequence-controlled polymers with distinct monomer patterning of dimethyl acrylamide and a bioinspired, structure-driving di(phenylalanine) acrylamide (FF). Sequence control was achieved through multiblock polymerizations, yielding unique ensembles of polymer sequences which were simulated by kinetic Monte Carlo simulations. Systematic analysis of the global (tertiary- and quaternary-like) structure in this amphiphilic copolymer series revealed the effect of multiple sequence descriptors: the number of domains, the hydropathy of terminal domains, and the patchiness (density) of FF within a domain, each of which impacted both chain collapse and the distribution of single- and multichain assemblies. Furthermore, both the conformational freedom of chain segments and local-scale, β-sheet-like interactions were sensitive to the patchiness of FF. To connect sequence, structure, and target function, we evaluated an additional series of nine sequence-controlled copolymers as sequestrants for rare earth elements (REEs) by incorporating a functional acrylic acid monomer into select polymer scaffolds. We identified key sequence variables that influence the binding affinity, capacity, and selectivity of the polymers for REEs. Collectively, these results highlight the potential of and boundaries of sequence control via multiblock polymerizations to drive primary sequence ensembles hierarchical structures, and ultimately the functionality of compositionally identical polymeric materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

An Antibody Cocktail-Based Immunoaffinity-LC-MS Method Enabled Ultra-Sensitive and Robust Quantification of Circulating Proinsulin Proteoforms and C-Peptide

Accurately measuring circulating proinsulin proteoforms is crucial for clinical investigation of diabetes, but was previously not feasible owing to limited assay specificity/sensitivity. Here, in this study, we devised a highly sensitive LC-MS-based strategy to quantify intact proinsulin, des-31,32 and des-64,65 proinsulin, and C-peptide in circulation. The method involves: (i) quantitative, robust affinity capture using an optimized antibody cocktail, eliminating the severe quantitative bias across multiple proteoforms typically introduced when using a single antibody; (ii) Lys-C digestion producing unique signature peptides for each proteoform, and (iii) trapping-nano-LC coupled with FAIMS/dCV-MS for an ultrasensitive analysis. The selective trapping/delivery ensured sensitive/selective analysis of the targets while achieving excellent analytical robustness that is critical for clinical assays, and the FAIMS/dCV substantially reduces baseline noise/interferences, further enhancing S/N. The assay achieved exceptional sensitivity, with serum LOQs of 1.7, 2.3, and 3.6 pg/mL respectively for intact-proinsulin, des-31,32 and des-64,65, representing the first assay capable of sensitively quantifying these major circulating proinsulin proteoforms. We applied this assay to 78 subjects, including autoantibody positive (n = 20) and new-onset type 1 diabetes (T1D, n = 19) with respective age/sex/BMI-matched controls, enabling the first accurate profiling of proinsulin proteoforms in clinical groups. The assay results demonstrated a clear separation of control and new-onset T1D groups that a parallel total-proinsulin ELISA assay fails to capture. Furthermore, distinct expression patterns in relative abundance ratios among proteoforms were observed across clinical groups. This assay may provide valuable insights into the β-cell functions and the onset/progression of diabetes and other associated conditions. Moreover, the strategy is broadly applicable to targeted measurement of other biomarker proteoforms.

Shen, Qingqing [University at Buffalo, NY (United ↗
DOE OSTI2023

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis -elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Short and medium range structure in elastic deformation of metallic and covalent glasses

Here, we present a concise methodology to analyze structural response to the applied stress in amorphous solids, including metallic glasses (MG), glassy selenium, silica and polycarbonate, using high energy x-ray diffraction and atomic pair distribution function (PDF) analysis. To assess the structural anisotropy induced by applied axial stress, diffraction data were expanded into spherical harmonics. Using Bessel transformation, components of the structure function were converted into isotropic and anisotropic PDFs. The PDFs were compared to the expected model behavior for ideal elastic deformation to separate homogeneous affine strain from local non-affine strains. In metallic glass the range of non-affine deformation is limited to the nearest neighbor shell, suggesting local strain relaxation under stress that occurs even in the elastic regime. Beyond the second atomic shell strain is uniform. However, in glassy silica, polycarbonate and selenium strong local bonding inhibits local displacements and strain in short range order is accommodated by rotation of local units. Interestingly, beyond a molecular unit, deformation in covalent systems is similar to MG, and response of the medium range order scales with the macroscopic stress.

glassy structure↗
DOE OSTI2020

Microscale thermophoresis as a powerful tool for screening glycosyltransferases involved in cell wall biosynthesis

Background: Identification and characterization of key enzymes associated with cell wall biosynthesis and modification is fundamental to gain insights into cell wall dynamics. However, it is a challenge that activity assays of glycosyltransferases are very low throughput and acceptor substrates are generally not available. Results: We optimized and validated microscale thermophoresis (MST) to achieve high throughput screening for glycosyltransferase substrates. MST is a powerful method for the quantitative analysis of protein-ligand interactions with low sample consumption. The technique is based on the motion of molecules along local temperature gradients, measured by fluorescence changes. We expressed glycosyltransferases as YFP-fusion proteins in tobacco and optimized the MST method to allow the determination of substrate binding affinity without purification of the target protein from the cell lysate. The application of this MST method to the β-1,4-galactosyltransferase AtGALS1 validated the capability to screen both nucleotide-sugar donor substrates and acceptor substrates. We also expanded the application to members of glycosyltransferase family GT61 in sorghum for substrate screening and function prediction. Conclusions: This method is rapid and sensitive to allow determination of both donor and acceptor substrates of glycosyltransferases. MST enables high throughput screening of glycosyltransferases for likely substrates, which will narrow down their in vivo function and help to select candidates for further studies. Additionally, this method gives insight into biochemical mechanism of glycosyltransferase function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Analysis of semivolatile organics in liquid radioactive residue using sorptive stir bar and solvent back-extraction

Current methods for semivolatiles analysis in radioactive samples can produce large volumes of radioactive solvent residue. A method utilizing stir-bar sorptive extraction has been explored in this work for its applicability to radioactive waste samples. This low solvent analytical method may accelerate remediation, minimize hazardous solvent waste, and reduce exposure risk to workers. Organic compounds (polyaromatic hydrocarbons, chlorinated aromatics, and phenolic compounds) were chosen as surrogates for common Liquid Waste System (LWS) contaminants at Savannah River Site (Aiken, SC). Stir-bar extraction parameters (extraction time, matrix modification, and effective pH range) and solvent back extraction parameters (solvent type, volume, and extraction time) were optimized experimentally for the chosen compounds. Affinity of the stir-bar extraction polymer to radionuclides Cs-137 and Am-241 was observed to determine radionuclide concentration effects. The stir-bar method achieved mean recovery of 100 ± 0.7% (1σ), relative to 114 ± 7% using solvent extraction, while reducing weekly method hands-on time by 93.4% and solvent volume consumption by 99.3%. Sensitivity was improved by 378% in simulated tank waste and 278% in real-world LWS matrix, relative to solvent extraction. This work has produced a safe and optimized method for the low solvent analysis of organics in legacy radioactive tank waste by stir-bar sorptive extraction.

GC-MS↗
DOE OSTI2024

Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics

Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the lambda-exchange of free energy perturbation (FEP). Further, two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/lambda-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.

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

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin

The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub 2 ) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub 2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub 2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub 2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

The Role of Functionalized Conducting Polymer Binders in Improving Power Density and Cycle Life of Lithium-Sulfur Batteries

Lithium-Sulfur batteries are promising as the next-generation of low-cost, high-energy rechargeable batteries. However, the commercialization of this battery has been limited by poor rate capability and cycle life. To improve the performance of Li-S cells, we have investigated the role of two n-dopable conducting polymers, N2200 and N2200-OE, as binders for the sulfur cathode. The electron and ion transport properties of these polymer binders, along with their strong affinity for polysulfides, results in significantly enhanced performance compared to cells with the traditional insulating PVDF binder. The role of these conducting polymer binders in enhancing the performance of the cells is analyzed using impedance spectroscopy, shuttle current measurements, conductivity measurements, UV–vis spectroscopy, GIWAXS studies and post-cycling analysis of the anodes. The conducting polymer binders reduce the cell impedance by a factor of four leading to a marked improvement in rate capability. The shuttling of the polysulfides and the formation of insoluble sulfides at the anode is curtailed by the interaction of the polysulfides with the backbone of the polymer binders, leading to an impressive capacity retention of 82% after 500 cycles. These studies demonstrate the benefit of tailored polymer binders at the sulfur electrode in addressing the limitations of lithium-sulfur batteries.

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

An isolated water droplet in the aqueous solution of a supramolecular tetrahedral cage

Water under nanoconfinement at ambient conditions has exhibited low-dimensional ice formation and liquid–solid phase transitions, but with structural and dynamical signatures that map onto known regions of water’s phase diagram. Using terahertz (THz) absorption spectroscopy and ab initio molecular dynamics, we have investigated the ambient water confined in a supramolecular tetrahedral assembly, and determined that a dynamically distinct network of 9 ± 1 water molecules is present within the nanocavity of the host. The low-frequency absorption spectrum and theoretical analysis of the water in the Ga 4 L 6 12– host demonstrate that the structure and dynamics of the encapsulated droplet is distinct from any known phase of water. A further inference is that the release of the highly unusual encapsulated water droplet creates a strong thermodynamic driver for the high-affinity binding of guests in aqueous solution for the Ga 4 L 6 12– supramolecular construct.

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

A human antibody epitope map of Pfs230D1 derived from analysis of individuals vaccinated with a malaria transmission-blocking vaccine

Pfs230 domain 1 (Pfs230D1) is an advanced malaria transmission-blocking vaccine antigen demonstrating high functional activity in clinical trials. However, the structural and functional correlates of transmission-blocking activity are not defined. Here, we characterized a panel of human monoclonal antibodies (hmAbs) elicited in vaccinees immunized with Pfs230D1. These hmAbs exhibited diverse transmission-reducing activity, yet all bound to Pfs230D1 with nanomolar affinity. We compiled epitope-binning data for seventeen hmAbs and structures of nine hmAbs complexes to construct a high-resolution epitope map and revealed that potent transmission-reducing hmAbs bound to one face of Pfs230D1, while non-potent hmAbs bound to the opposing side. The structure of Pfs230D1D2 revealed that non-potent transmission-reducing epitopes were occluded by the second domain. The hmAb epitope map delineated binary hmAb combinations that synergized for extremely high-potency, transmission-reducing activity. Finally, this work provides a high-resolution guide for structure-based design of enhanced immunogens and informs diagnostics that measure the transmission-reducing response.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Reversible Binding Interfaces Made of Microstructured Polymer Brushes

The polymer brush architecture of the end-tethered polymer molecules is one of the most widely used efficient methods to regulate interfacial interactions in colloidal systems found in live matter and manufactured materials. Emerging applications of polymer brush structures require solutions to new tasks in the control of interfacial interactions. The rapid development of live cell manufacturing relies on scalable and efficient cell harvesting methods. Stimuli-responsive surfaces made of surface-grafted poly(N-isopropylacrylamide) (PNIPAM) can bind and detach the adherent cell upon changes in temperature and have been used for cell growth and harvesting. The applications are limited by the requirement to satisfy a range of PNIPAM coating characteristics that depend on the dimensions of the integrin complex in the cell membrane and the basal surface. The analysis of the microstructured surfaces, when adhesive and disjoining functions of the microdomains are decoupled, shows that many limitations of PNIPAM one-component coatings can be avoided by using a much broader range of structural characteristics of the microstructured interfaces composed of alternating disjoining PNIPAM domains and adhesive polymeric domains with cell-affinity functional groups. Temperature-controlled reversible adhesion to such microstructured interfaces is studied here experimentally with model systems of solid spherical particles and by employing simulations for solid and soft membranes interacting with the microstructured surfaces to mimic interactions with soft and solid disk-like particles.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Measurement of isosteric heat of gas adsorption and Brunauer–Emmett–Teller (BET) surface area using a quartz crystal microbalance

The study of gas adsorption on a solid surface evaluates the affinity between sorbate gas and sorbent substrate and factors that contribute to this. This report presents a test platform for adsorption experiments of various gases on various solid surfaces. Controlled environmental conditions enable investigations in materials surface science and increase the consistency among adsorption data. The system utilizes a quartz crystal microbalance to perform gravimetric analysis of deposition and adsorption, enabling investigation of the interaction of gaseous molecules with solid surfaces. In this study, a quartz crystal microbalance as gas adsorption detector was integrated with an environmental chamber to create a versatile tool for gas adsorption experiments on thin films. Experimental operation of this apparatus was demonstrated via acquisition of the adsorption isotherms of cyclohexane vapor on a gold surface at 55 and 70 °C. The result indicated International Union of Pure and Applied Chemistry Type II adsorption. Consequentially, application of the Brunauer–Emmett–Teller model to the isotherm data subject to predefined criteria for linear region selection yielded a surface area of the sorbent of 0.53 cm2 at 55 °C. From the monolayer region of the isotherms, the isosteric heat of adsorption of the cyclohexane vapor on gold was calculated to be 37 kJ mol-1.

47 OTHER INSTRUMENTATION↗