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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
NASA NTRS2000

Molecular and biochemical evidence for the involvement of calcium/calmodulin in auxin action

The use of (35)S-labeled calmodulin (CaM) to screen a corn root cDNA expression library has led to the isolation of a CaM-binding protein, encoded by a cDNA with sequence similarity to small auxin up RNAs (SAURs), a class of early auxin-responsive genes. The cDNA designated as ZmSAUR1 (Zea mays SAURs) was expressed in Escherichia coli, and the recombinant protein was purified by CaM affinity chromatography. The CaM binding assay revealed that the recombinant protein binds to CaM in a calcium-dependent manner. Deletion analysis revealed that the CaM binding site was located at the NH(2)-terminal domain. A synthetic peptide of amino acids 20-45, corresponding to the potential CaM binding region, was used for calcium-dependent mobility shift assays. The synthetic peptide formed a stable complex with CaM only in the presence of calcium. The CaM affinity assay indicated that ZmSAUR1 binds to CaM with high affinity (K(d) approximately 15 nM) in a calcium-dependent manner. Comparison of the NH(2)-terminal portions of all of the characterized SAURs revealed that they all contain a stretch of the basic alpha-amphiphilic helix similar to the CaM binding region of ZmSAUR1. CaM binds to the two synthetic peptides from the NH(2)-terminal regions of Arabidopsis SAUR-AC1 and soybean 10A5, suggesting that this is a general phenomenon for all SAURs. Northern analysis was carried out using the total RNA isolated from auxin-treated corn coleoptile segments. ZmSAUR1 gene expression began within 10 min, increased rapidly between 10 and 60 min, and peaked around 60 min after 10 microM alpha-naphthaleneacetic acid treatment. These results indicate that ZmSAUR1 is an early auxin-responsive gene. The CaM antagonist N-(6-aminohexyl)5-chloro-1-naphthalenesulfonamide hydrochloride inhibited the auxin-induced cell elongation but not the auxin-induced expression of ZmSAUR1. This suggests that calcium/CaM do not regulate ZmSAUR1 at the transcriptional level. CaM binding to ZmSAUR1 in a calcium-dependent manner suggests that calcium/CaM regulate ZmSAUR1 at the post-translational level. Our data provide the first direct evidence for the involvement of calcium/CaM-mediated signaling in auxin-mediated signal transduction.

NASA Program Fundamental Space Biology↗
NASA NTRS1999

CCAAT/enhancer-binding protein delta is a critical regulator of insulin-like growth factor-I gene transcription in osteoblasts

Insulin-like growth factor-I (IGF-I) plays a major role in promoting skeletal growth by stimulating bone cell replication and differentiation. Prostaglandin E2 and other agents that induce cAMP production enhance IGF-I gene transcription in cultured rat osteoblasts through a DNA element termed HS3D, located in the proximal part of the major rat IGF-I promoter. We previously determined that CCAAT/enhancer-binding protein delta (C/EBPdelta) is the key cAMP-stimulated regulator of IGF-I transcription in these cells and showed that it transactivates the rat IGF-I promoter through the HS3D site. We now have defined the physical-chemical properties and functional consequences of the interactions between C/EBPdelta and HS3D. C/EBPdelta, expressed in COS-7 cells or purified as a recombinant protein from Escherichia coli, bound to HS3D with an affinity at least equivalent to that of the albumin D-site, a known high affinity C/EBP binding sequence, and both DNA elements competed equally for C/EBPdelta. C/EBPdelta bound to HS3D as a dimer, with protein-DNA contact points located on guanine residues on both DNA strands within and just adjacent to the core C/EBP half-site, GCAAT, as determined by methylation interference footprinting. C/EBPdelta also formed protein-protein dimers in the absence of interactions with its DNA binding site, as indicated by results of glutaraldehyde cross-linking studies. As established by competition gel-mobility shift experiments, the conserved HS3D sequence from rat, human, and chicken also bound C/EBPdelta with similar affinity. We also found that prostaglandin E2-induced expression of reporter genes containing human IGF-I promoter 1 or four tandem copies of the human HS3D element fused to a minimal promoter and show that these effects were enhanced by a co-transfected C/EBPdelta expression plasmid. Taken together, our results provide evidence that C/EBPdelta is a critical activator of IGF-I gene transcription in osteoblasts and potentially in other cell types and species.

NASA Discipline Musculoskeletal↗
NASA NTRS1996

Approximate scaling properties of RNA free energy landscapes

RNA free energy landscapes are analysed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics as free random walks. We find that an AR(1) time series is in general approximately self-affine on timescales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.

Signal Processing, Computer-Assisted↗
DOE OSTI2020

Methods and materials for determination of distribution coefficients for separation materials

Methods and materials for determining the affinity of separation materials for targeted species are described. A composite separation medium is described that combines a separation material such as an ion exchange material or a sorbent with an SERS substrate. Methods and materials can be utilized to determine the distribution coefficient of a species for a separation material after running a single separation protocol followed by examination of the separation material of the protocol according to SERS. Disclosed methods can be utilized to determine the affinity of existing separation materials for targeted species as well as to determine the affinity of newly engineered separation materials to characterize species.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Synergetic Effects of Soil Organic Matter Components During Interactions with Minerals

Mineral-associated soil organic matter (SOM) is critical for stabilizing organic carbon and mitigating climate change. However, mineral-SOM interactions at the molecular scale, particularly synergetic adsorption through organic-organic interaction on the mineral surface known as organic multilayering, remain poorly understood. This study investigates the impact of organic multilayering on mineral-SOM interactions, by integrating macroscale experiments and molecular-scale simulations that assess the individual and sequential adsorption of major SOM compounds – lauric acid (lipid), pentaglycine (amino acid), trehalose (carbohydrate), and lignin onto soil minerals. Ferrihydrite, Al-hydroxide, and calcite are exposed to SOM compounds to determine adsorption affinities and binding energies. Results show that lauric acid has 20-40 times higher K d than pentaglycine, following the order K d (ferrihydrite) > K d (Al-hydroxide) >> K d (calcite). Molecular-scale simulations confirm that lauric acid has a higher binding energy (30.8 kcal/mol) on ferrihydrite than pentaglycine (6.0 kcal/mol), attributed to lipid hydrophobicity. The lower binding energy of pentaglycine results from its hydrophilic amide groups, facilitating partitioning into water. Sequential experiments examine how the first layer of lipid or amino acid affects the adsorption of carbohydrate/lignin, which show little or no individual adsorption affinities. Macroscale results reveal that lipid and amino acid adsorption induce ferrihydrite particle repulsion increasing reactive surface area and enhancing carbohydrate/lignin adsorption independently and synergistically through organic multilayering. Molecular-scale results reveal that amino acid adsorbed on ferrihydrite interacts more readily with lignin macroaggregates (preformed in solution) than with individual lignin units, indicating organic multilayering via H-bonding. Further, these findings reveal the molecular mechanisms of SOM-mineral interactions, crucial for enhancing soil carbon stabilization.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. In this work, we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Binding of actin to lens alpha crystallins

Actin has been coupled to a cyanogen bromide-activated Sepharose 4B column, then tested for binding to alpha, beta, and gamma crystallin preparations from the bovine lens. Alpha, but not beta or gamma, crystallins bound to the actin affinity column in a time dependent and saturable manner. Subfractionation of the alpha crystallin preparation into the alpha-A and alpha-B species, followed by incubation with the affinity column, demonstrated that both species bound approximately the same. Together, these studies demonstrate a specific and saturable binding of lens alpha-A and alpha-B with actin.

NASA Discipline Cell Biology↗
DOE OSTI2022

Top Stack Optimization for Cu 2 BaSn(S, Se) 4 Photovoltaic Cell Leads to Improved Device Power Conversion Efficiency beyond 6%

Earth-abundant and air-stable Cu 2 BaSnS 4-x Se x (CBTSSe) and related thin-film absorbers are regarded as prospective options to meet the increasing demand for low-cost solar cell deployment. Devices based on vacuum-deposited CBTSSe absorbers have achieved record power conversion efficiency (PCE) of 5.2 % based on a conventional device structure using CdS buffer and i-ZnO/ITO window layers, with open-circuit voltage (V OC ) posing the major bottleneck for improving solar cell performance. The current study demonstrates a >20 % improvement in V OC (from 0.62 V to 0.75 V) and corresponding enhancement in PCE (from 5.1 % to 6.2 % without anti-reflection coating; to 6.5 % with MgF 2 anti-reflection coating) for solution-deposited CBTSSe solar cells. This performance improvement is realized by introducing an alternative successive ionic layer adsorption and reaction (SILAR)-deposited Zn 1-x Cd x S buffer combined with sputtered Zn 1-x Mg x O/Al-doped ZnO window/top contact layer, which offer lower electron affinities relative to the conventional CdS/i-ZnO/ITO stack and better matching with the low electron affinity of CBTSSe. A combined experimental (temperature- and light intensity-dependent V OC measurements) and device simulation (SCAPS-1D) evaluation points to the importance of addressing relative band offsets for both the buffer and window layers relative to the absorber in mitigating interfacial recombination and optimizing CBTSSe solar cell performance.

25 ENERGY STORAGE↗
DOE OSTI2020

Sulfonyl PIM–1: A diverse separation membrane with dilation resistance

A sulfone modified variant (soPIM–1) of the first polymer of intrinsic microporosity has been studied through molecular simulations to analyze its applicability for adsorption–based separations of diverse nonpolar, quadrupolar, and dipolar adsorbate species. Single component gas phase adsorption isotherms of each adsorbate are provided. Here, the adsorptive properties of soPIM–1 are reported from the application of two methods: (a) traditional grand canonical Monte Carlo (GCMC) simulations and (b) a combination of Monte Carlo and molecular dynamics (GCMC/MD) techniques, which accounts for sorption–induced polymer dynamics. The calculated isosteric heats of adsorption are compared to those from the parent PIM–1 structure and reveals increased CO2 affinity with relatively no change in hydrocarbon affinity. Moreover, to quantify soPIM–1's resistance to dilation the evolution of the microporous structure across the adsorption isotherm loading pressures has been evaluated. Relatedly, nonequilibrium MD simulations have been utilized to determine that soPIM–1 is approximately twice as stiff as PIM–1.

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

CO 2 Capture by Hybrid Ultramicroporous TIFSIX‐3‐Ni under Humid Conditions Using Non‐Equilibrium Cycling

Abstract Although pyrazine‐linked hybrid ultramicroporous materials (HUMs, pore size <7 Å) are benchmark physisorbents for trace carbon dioxide (CO 2 ) capture under dry conditions, their affinity for water (H 2 O) mitigates their carbon capture performance in humid conditions. Herein, we report on the co‐adsorption of H 2 O and CO 2 by TIFSIX‐3‐Ni—a high CO 2 affinity HUM—and find that slow H 2 O sorption kinetics can enable CO 2 uptake and release using shortened adsorption cycles with retention of ca. 90 % of dry CO 2 uptake. Insight into co‐adsorption is provided by in situ infrared spectroscopy and ab initio calculations. The binding sites and sorption mechanisms reveal that both CO 2 and H 2 O molecules occupy the same ultramicropore through favorable interactions between CO 2 and H 2 O at low water loading. An energetically favored water network displaces CO 2 molecules at higher loading. Our results offer bottom‐up design principles and insight into co‐adsorption of CO 2 and H 2 O that is likely to be relevant across the full spectrum of carbon capture sorbents to better understand and address the challenge posed by humidity to gas capture.

Ullah, Saif↗
DOE OSTI2025

Catching Fullerenes: Synthesis of Molecular Nanogloves

Abstract Herein, we report the synthesis of a new series of rigid, all meta ‐phenylene, conjugated deep‐cavity molecules, displaying high binding affinity towards buckyballs. A facile synthetic approach with an overall combined yield of approximately 53% in the last two steps has been developed using a templating strategy that combines the general structure of resorcin[4]arene and [12]cyclo‐ meta ‐phenylene. These two moieties are covalently linked via four acetal bonds, resulting in a glove‐like architecture. 1 H NMR titration experiments reveal fullerene binding affinities ( K a ) exceeding ≥10 6 M −1 . The size complementarity between fullerenes and these scaffolds maximizes CH⋯π and π⋯π interactions, and their host:guest adduct resembles a ball in a glove, hence their name as nanogloves. Fullerene recognition is tested by suspending carbon soot in a solution of nanoglove in 1,1,2,2‐tetrachloroethane, where more than a dozen fullerenes are observed, ranging from C 60 to C 96 .

Mirzaei, Saber [Department of Chemistry Rice Unive↗
DOE OSTI2022

CO 2 Capture by Hybrid Ultramicroporous TIFSIX‐3‐Ni under Humid Conditions Using Non‐Equilibrium Cycling

Abstract Although pyrazine‐linked hybrid ultramicroporous materials (HUMs, pore size <7 Å) are benchmark physisorbents for trace carbon dioxide (CO 2 ) capture under dry conditions, their affinity for water (H 2 O) mitigates their carbon capture performance in humid conditions. Herein, we report on the co‐adsorption of H 2 O and CO 2 by TIFSIX‐3‐Ni—a high CO 2 affinity HUM—and find that slow H 2 O sorption kinetics can enable CO 2 uptake and release using shortened adsorption cycles with retention of ca. 90 % of dry CO 2 uptake. Insight into co‐adsorption is provided by in situ infrared spectroscopy and ab initio calculations. The binding sites and sorption mechanisms reveal that both CO 2 and H 2 O molecules occupy the same ultramicropore through favorable interactions between CO 2 and H 2 O at low water loading. An energetically favored water network displaces CO 2 molecules at higher loading. Our results offer bottom‐up design principles and insight into co‐adsorption of CO 2 and H 2 O that is likely to be relevant across the full spectrum of carbon capture sorbents to better understand and address the challenge posed by humidity to gas capture.

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

Chelator‐Assisted Precipitation‐Based Separation of the Rare Earth Elements Neodymium and Dysprosium from Aqueous Solutions

The rare earth elements (REEs) are critical resources for many clean energy technologies, but are difficult to obtain in their elementally pure forms because of their nearly identical chemical properties. Here, an analogue of macropa, G-macropa, was synthesized and employed for an aqueous precipitation-based separation of Nd 3+ and Dy 3+ . G-macropa maintains the same thermodynamic preference for the large REEs as macropa, but shows smaller thermodynamic stability constants. Molecular dynamics studies demonstrate that the binding affinity differences of these chelators for Nd 3+ and Dy 3+ is a consequence of the presence or absence of an inner-sphere water molecule, which alters the donor strength of the macrocyclic ethers. Leveraging the small REE affinity of G-macropa, we demonstrate that within aqueous solutions of Nd 3+ , Dy 3+ , and G-macropa, the addition of HCO 3 − selectively precipitates Dy 2 (CO 3 ) 3 , leaving the Nd 3+ −G-macropa complex in solution. With this method, remarkably high separation factors of 841 and 741 are achieved for 50 : 50 and 75 : 25 mixtures. Further studies involving Nd 3+ :Dy 3+ ratios of 95 : 5 in authentic magnet waste also afford an efficient separation as well. Finally, G-macropa is recovered via crystallization with HCl and used for subsequent extractions, demonstrating its good recyclability.

Gao, Yangyang↗
DOE OSTI2020

Identification of preferred multimodal ligand‐binding regions on IgG1 F C using nuclear magnetic resonance and molecular dynamics simulations

Abstract In this study, the binding of multimodal chromatographic ligands to the IgG1 F C domain were studied using nuclear magnetic resonance and molecular dynamics simulations. Nuclear magnetic resonance experiments carried out with chromatographic ligands and a perdeuterated 15 N‐labeled F C domain indicated that while single‐mode ion exchange ligands interacted very weakly throughout the F C surface, multimodal ligands containing negatively charged and aromatic moieties interacted with specific clusters of residues with relatively high affinity, forming distinct binding regions on the F C . The multimodal ligand‐binding sites on the F C were concentrated in the hinge region and near the interface of the C H 2 and C H 3 domains. Furthermore, the multimodal binding sites were primarily composed of positively charged, polar, and aliphatic residues in these regions, with histidine residues exhibiting some of the strongest binding affinities with the multimodal ligand. Interestingly, comparison of protein surface property data with ligand interaction sites indicated that the patch analysis on F C corroborated molecular‐level binding information obtained from the nuclear magnetic resonance experiments. Finally, molecular dynamics simulation results were shown to be qualitatively consistent with the nuclear magnetic resonance results and to provide further insights into the binding mechanisms. An important contribution to multimodal ligand‐F C binding in these preferred regions was shown to be electrostatic interactions and π–π stacking of surface‐exposed histidines with the ligands. This combined biophysical and simulation approach has provided a deeper molecular‐level understanding of multimodal ligand–F C interactions and sets the stage for future analyses of even more complex biotherapeutics.

Gudhka, Ronak B.↗
DOE OSTI2020

Reduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activity

Dissociation of nonproductively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling nonproductive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three models type-A CBMs (Families 1, 3a, and 64) tethered to multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE–CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation were employed to measure CBM adsorption and desorption rate constants kon and koff, respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates (koff) and reduced effective adsorption rates (nkon), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in nonproductive enzyme binding and develop improved cellulolytic enzymes for industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Route to Design Novel Functional Peptides by Applying a Denoising Diffusional Model to mRNA Display Libraries

In vitro directed evolution techniques, such as mRNA display, enable peptide ligand discovery and optimization. However, physical libraries that rely on a genetic code can only search a small fraction of sequence space due to inherent biases in the genetic code and experimental limitations. To address this challenge, denoising diffusion implicit models (DDIMs) are applied to generate novel peptide ligands against B‐cell lymphoma extra‐large (Bcl‐x L ), a key cancer target. Starting with high‐throughput sequencing data from previous selections, a DDIM is trained to produce novel sequences with high affinity binding. Experimental validation confirms that most generated sequences are functionally equivalent to the original library members for Bcl‐x L binding and demonstrated comparable binding kinetics and affinity relative to the wildtype and nearest original neighbors. Importantly, this approach generated rare sequences not easily accessible via mutation and directed evolution. These results indicate that DDIMs can complement and expand directed evolution data, efficiently exploring underrepresented regions of sequence space. This approach provides a broadly applicable framework for accelerating ligand discovery and optimizing molecular properties across diverse targets.

Qi, Pearl [Mork Family Department of Chemical Engi↗
DOE OSTI2025

The Role of Asparagine as a Gatekeeper Residue in the Selective Binding of Rare Earth Elements by Lanthanide‐Binding Peptides

Abstract Lanthanide‐binding tag (LBT) peptides selectively complex lanthanide cations (Ln 3+ ) in their binding pockets and are promising for lanthanide separation. However, designing LBTs that selectively target specific Ln 3+ cations remains a challenge due to limited molecular‐level understanding and control of interactions within the lanthanide‐binding pocket. In this study, we reveal that the N5 asparagine residue acts as a gatekeeper in the binding pocket, resulting in a 100‐fold selectivity for smaller Lu 3+ over larger La 3+ cations. Nuclear magnetic resonance spectroscopy and molecular dynamics simulations show that the N5 residue weakly binds to the larger La 3+ cation, permitting H 2 O molecules inside the pocket. For the smaller Lu 3+ cations, the N5 residue forms an inter‐arm hydrogen bond with the E14 glutamic acid residue, locking the Lu 3+ cation in the pocket and preventing H 2 O infiltration. Mutating the N5 asparagine to a D5 aspartic acid prevents such a hydrogen bond, eliminating the gatekeeping mechanism and precipitously reducing selectivity. The resulting binding affinity to Ln 3+ cations is non‐monotonic but generally increases with cation size. These results suggest a molecular design paradigm: the reduced affinity for larger lanthanides is due to open pocket conformations, while the selectivity of smaller Ln 3+ cations over larger ones is due to the gatekeeping hydrogen bond.

Chemistry↗
DOE OSTI2026

Charge Density Mismatch is a Key Characteristic of Highly Concentrated Electrolyte Solutions and Highly Water‐Soluble Salts

Only very soluble electrolytes can form concentrated solutions. Some salts are so soluble that there are less than four water molecules per ion in saturated solution. Ions usually form clusters or networks with more than one counterion in their coordination sphere in these concentrated solutions. Do these ultraconcentrated solutions form because the counterions have high affinity for each other in liquid, or because they have a poor affinity for each other in solids? Here, in this study, this question is addressed using the valence matching principle of the bond valence model by comparing the charge density mismatch between counterions to their solubility for a series of alkali fluorides, carboxylates, and oxyanions. The solubilities are plotted against the characteristic average bond valence of the alkali, and the lowest solubilities are those where alkali and anion had matching bond valences. Conversely, the highest solubilities are those with poorly matching bond valences. Available ion-pairing constants indicate that the weakest ion-pairs are those with the largest bond valence mismatch, indicating that the large water solubilities occur despite weak ion-pairing rather than because of strong ion-pairing. Therefore, a key characteristic of highly water-soluble salts is that the counterions have mismatched charge densities.

concentrated solutions↗