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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Resolving SPARC–HSA binding kinetics with an ultrasensitive photonic sensor based on bound states in the continuum

Secreted protein acidic and rich in cysteine (SPARC) is critical in cell-matrix interactions and tissue remodeling. It influences tumor progression through its affinity for human serum albumin (HSA) - the most abundant plasma protein, which also plays a crucial role in drug delivery. Strong molecular binding leads to a dissociation constant KD in the nanomolar range. Thus, determining KD requires detecting sub-nanomolar concentrations with ultrasensitive methods. This may be crucial for elucidating the nature of SPARC-HSA binding, as their interaction remains a subject of debate. Capturing these interactions accurately requires a platform capable of resolving rapid binding kinetics at extremely low analyte concentrations. In this work, we report on a microfluidics-integrated photonic nanostructure that supports bound states in the continuum (BICs) and is optimized for studying the fast kinetics of high-affinity protein-protein interactions. The unprecedented capability of detecting sub-nanomolar concentrations allows quantifying KD between SPARC and HSA beyond the state of the art. We leverage an all-dielectric photonic crystal slab (PhCS) sustaining two BIC branches arising from gapped Dirac cone dispersion. HSA is covalently immobilized on the PhCS bonded to a PDMS microfluidic chamber. SPARC dissociation is carried out using PBS buffer (pH 7.4), ensuring complete protein release through precise control of the flow rate and continuous spectral monitoring of the BICs. The measured KD=8.2±0.8 nM confirms the strong affinity of SPARC for HSA. This study highlights the potential of BIC-based sensing as a versatile tool for investigating protein interactions. These results also have implications for the optimization of drug delivery systems and cancer treatment strategies.

Albumin↗
DOE OSTI2020

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

We report analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Influence of pH on chloride binding isotherms for cement paste and its components

In this paper, chloride (Cl{sup −}) binding isotherms are developed for cement hydration compounds, specifically, calcium-silicate-hydrates (CSH) and AFm phases including mono-sulfate aluminate, hydroxy-AFm, monocarbonate-AFm, and hemicarbonate-AFm, in simulated concrete pore solutions to account for the effect of pH and the presence of other ions. pH and the presence of other ions have a strong influence on the Cl{sup −} binding capacity of cement compounds, which have not been taken into consideration in previous research. A novel experimental technique is developed to characterize the binding capacity from very low (1 mM) to very high concentrations (5 M). To overcome the existing challenges of measuring both low and high Cl{sup −} concentrations without significant dilution and in the presence of SO{sub 4}{sup 2−} and OH{sup −} ions, a potentiometric method was used. The amorphous CSH in the hydrated cement paste; thus, the heterogeneity of the hydrated components of the cement paste was also quantified and accounted for in this study.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Medium-independent hydrogen atom binding isotherms of nickel oxide electrodes

Adsorption and transfer of hydrogen atoms at solid/solution interfaces are fundamental to heterogeneous catalysis for chemical energy transformations and other processes. Reported here are electrochemical and spectroelectrochemical measurements of the thermodynamics of H-atom binding to nickel oxide electrodes, both the average and the distribution of NiO–H bond dissociation free energies (BDFEs). These are perhaps the first measurements of binding isotherms at non-metal electrodes. Remarkably, both the BDFEs and the non-Langmuirian isotherms are the same in water, acetonitrile, and dimethylformamide, and with different buffers and proton activities. Such medium independence of the BDFEs and isotherms has not been previously reported for any binary material. The medium independence supports the common use of computed hydrogen binding energies as intrinsic descriptors of surface reactivity, while the broadened isotherms add a level of complexity to such analyses. Furthermore, this work demonstrates the capability to derive key thermodynamic parameters at chemically reactive solid-liquid interfaces.

13 HYDRO ENERGY↗
DOE OSTI2021

Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center

Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O 2 -binding site. Supporting HYSCORE spectroscopic experiments were performed on the (3MPA/NO)-bound Av3MDO iron nitrosyl (S = 3/2) site. In combination with spectroscopic simulations and optimized DFT models, this work provides an experimentally verified model of the Av3MDO enzyme–substrate complex, effectively resolving a debate in the literature regarding the preferred substrate-binding denticity. These results elegantly explain the observed 3MDO substrate specificity, but leave unanswered questions regarding the mechanism of substrate-gated reactivity with dioxygen.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors

The low-density lipoprotein receptor (LDLR) family of receptors are cell-surface receptors that internalize numerous ligands and play crucial role in various processes, such as lipoprotein metabolism, hemostasis, fetal development, etc. Previously, receptor-associated protein (RAP) was described as a molecular chaperone for LDLR-related protein 1 (LRP1), a prominent member of the LDLR family. We aimed to verify this role of RAP for LRP1 and two other LDLR family receptors, LDLR and vLDLR, and to investigate the mechanisms of respective interactions using a cell culture model system, purified system, and in silico modelling. Upon coexpression of RAP with clusters of the ligand-binding complement repeats (CRs) of the receptors in secreted form in insect cells culture, the isolated proteins had increased yield, enhanced folding, and improved binding properties compared with proteins expressed without RAP, as determined by circular dichroism and surface plasmon resonance. Within LRP1 CR-clusters II and IV, we identified multiple sites comprised of adjacent CR doublets, which provide alternative bivalent binding combinations with specific pairs of lysines on RAP. Mutational analysis of these lysines within each of isolated RAP D1/D2 and D3 domains having high affinity to LRP1 and of conserved tryptophans on selected CR-doublets of LRP1, as well as in silico docking of a model LRP1 CR-triplet with RAP, indicated a universal role for these residues in interaction of RAP and LRP1. Consequently, we propose a new model of RAP interaction with LDLR family receptors based on switching of the bivalent contacts between molecules over time in a dynamic mode.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Binding of radionuclides and surrogate to 18-crown-6 ether by density functional theory

For this work, we use density functional theory to investigate the interactions of cerium, americium, and curium cations with crown ethers. Our calculations reveal that the modeled structure of cerium integrated within the crown ether is in good agreement with experimental data, with the negative binding energy indicating that capturing the cerium nitrates is thermodynamically favorable. Our results demonstrate that crown ethers can also bind americium and curium, providing insights into the potential applications of crown ether in radionuclide sequestration. Finally, we explore the impact of the skeleton modification of different crown ethers through by substitution of nitrogen atoms in the core of the crown ether for oxygen atoms and find that this structural modification significantly increases the radionuclide binding energies. These findings provide insights on the potential for the use of organic linkers such as crown ethers to address the urgent needs in radionuclide sequestration, separation and sensing.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Changes in nitrate binding with lanthanides in BLPhen complexes

Preorganized ligands such as bis-lactam-1,10-phenanthroline (BLPhen) offer unique selectivity trends in solvent extraction of rare-earth ions, particularly from aqueous nitrate solutions. However, due to the ligand’s lipophilicity it is experimentally challenging to obtain crystal structures of the corresponding lanthanide (Ln):ligand complexes to describe the local structure of the first coordination shell and the role of the nitrate ions in the organic phase. In this work, we report first principles molecular dynamics (FPMD) simulations of the complexation of trivalent lanthanide ions (La, Nd, and Eu) with the BLPhen ligand in the presence of nitrate ions in the dichloroethane (DCE) solvent. We find that two nitrate anions are present in the first solvation shell and the third nitrate anion is far from the first solvation shell in all three [Ln(BLPhen) 2 ] 3+ complexes examined. Moving along the lanthanide series from La to Nd to Eu, the binding pocket formed by the two BLPhen ligands shrinks in size; as a result, the two nitrate configuration changes from one-monodentate/one-bidentate binding mode for La and Nd to all monodentate for Eu. Meanwhile, the total coordination number drops from 11 for La and Nd to 10 for Eu. More interestingly, the bidentate binding in [La(BLPhen) 2 ] 3+ and [Nd(BLPhen) 2 ] 3+ complexes is highly dynamic, frequently switching to monodentate and back. The FPMD insights into the differing modes and dynamics of nitrates in the first coordination shell will be useful for further atomistic understanding of the complex structure, formation, and stability in the organic phase.

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

Determining the domain-level reaction-diffusion properties of an actin-binding protein transgelin-2 within cells

Proteins in cells undergo repeated binding to other molecules, thereby reducing the apparent extent of their intracellular diffusion. While much effort has been made to analytically decouple these combined effects of pure diffusion and chemical binding, it is difficult with conventional approaches to attribute the measured quantities to the nature of specific domains of the proteins. Motivated by the common goal in cell signaling research aimed at identifying the domains responsible for particular intermolecular interactions, here we describe a framework for determining the local physicochemical properties of cellular proteins associated with immobile scaffolds. To validate this new approach, we apply it to transgelin-2, an actin-binding protein whose intracellular dynamics remains elusive. We develop a fluorescence recovery after photobleaching (FRAP)-based framework, in which comprehensive combinations of domain-deletion mutants are created, and the difference among them in FRAP response is analyzed. We demonstrate that transgelin-2 in actin stress fibers (SFs) interacts with F-actin via two separate domains, and the chemical properties are determined for the individual domains. Its pure diffusion properties independent of the association to F-actin is also obtained. Our approach will thus be useful, as presented here for transgelin-2, in addressing the signaling mechanism of cellular proteins associated with SFs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Short-Term Inhibition and Long-Term Enhancement of Irreversible Trace Metal Binding to Goethite in Multi-Metal Systems

Iron (oxyhydr)oxide minerals are important sorbents of trace metals in aquatic environments. Adsorption–desorption hysteresis has been documented for trace metals after aging, suggesting that they become incorporated over time. We previously found that ion size controls the extent of irreversible metal binding of single metals to goethite. In this study, we evaluate how the presence of multiple metals influences irreversible binding. Mixed Ni–Zn and Ni–Cd solutions were aged with goethite at pH 7 for 2 days, 30 days, and 60 days, after which isotope exchange experiments were performed to assess the lability of the adsorbed metal pools. After 2 days of aging, Ni and Cd in mixed-metal systems were more labile than in single-metal systems, indicating that competitive adsorption may partially block irreversible binding on short time scales. After 60 days, all three metals had larger irreversibly bound fractions than in single-metal systems. X-ray absorption near-edge structure (XANES) spectroscopy indicates that irreversibly bound fractions correlate with incorporation into goethite. This study demonstrates that pools of coadsorbed metals are bioaccessible on a time scale of minutes. Cooperative effects promote the structural sequestration of even large trace metals, causing reactive transport models to likely overpredict metal mobility. Long-term metal entrapment processes hinder micronutrient availability, impact contaminant sequestration and critical mineral recovery, and yield complex pathways through which metal solubilization may be enhanced or hindered during redox cycling.

58 GEOSCIENCES↗
DOE OSTI2021

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand–protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

The accurate and reliable prediction of protein–ligand binding affinities can play a central role in the drug discovery process as well as in personalized medicine. Of considerable importance during lead optimization are the alchemical free energy methods that furnish an estimation of relative binding free energies (RBFE) of similar molecules. Recent advances in these methods have increased their speed, accuracy, and precision. This is evident from the increasing number of retrospective as well as prospective studies employing them. However, such methods still have limited applicability in real-world scenarios due to a number of important yet unresolved issues. Here, we report the findings from a large data set comprising over 500 ligand transformations spanning over 300 ligands binding to a diverse set of 14 different protein targets which furnish statistically robust results on the accuracy, precision, and reproducibility of RBFE calculations. We use ensemble-based methods which are the only way to provide reliable uncertainty quantification given that the underlying molecular dynamics is chaotic. These are implemented using TIES (Thermodynamic Integration with Enhanced Sampling). Results achieve chemical accuracy in all cases. Ensemble simulations also furnish information on the statistical distributions of the free energy calculations which exhibit non-normal behavior. We find that the “enhanced sampling” method known as replica exchange with solute tempering degrades RBFE predictions. We also report definitively on numerous associated alchemical factors including the choice of ligand charge method, flexibility in ligand structure, and the size of the alchemical region including the number of atoms involved in transforming one ligand into another. Our findings provide a key set of recommendations that should be adopted for the reliable application of RBFE methods.

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

Protein–Ligand Binding Free-Energy Calculations with ARROW–A Purely First-Principles Parameterized Polarizable Force Field

Protein–ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)–a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein–ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ~0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields.

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

Atomistic Insight into Cation Effects on Binding Energies in Cu-Catalyzed Carbon Dioxide Reduction

Electrolyte properties in general and electrolyte ions in particular have been shown to have significant effects on the kinetics of electrochemical CO 2 and CO reduction at metal electrodes, but these effects have not yet been fully understood. Here, we investigate the effects of cations at the aqueous electrolyte–Cu(211) interface on adsorbate binding energies and the electrolyte structure using density functional theory (DFT). Charging the interface via explicit Na + has systematic effects on adsorbate–electrolyte interactions and conformations. We describe specific local adsorbate–ion interactions, including direct alkali ion–adsorbate coordination and hydrogen bonding via ion-coordinated water molecules. The relative importance of these specific interactions and purely electrostatic field–adsorbate interactions is investigated by comparing the DFT-calculated ion effects to those predicted by purely electrostatic models of the interface and the adsorbates. We find that the trend in ion effects among different adsorbates at constant surface charge density is well explained by a purely electrostatic interaction model. The binding energy of OCCHO is found to depend strongly on the surface charge density as well as the spatial distribution of ions at constant surface charge density. These effects are also explained by a purely electrostatic local electrostatic field–adsorbate model. This indicates that alkali ion effects can be mainly attributed to purely electrostatic field interactions and that the local field at ion-stabilized active sites can depend significantly on both the overall charge density and on the spatial distribution of ions at constant charge density. This work provides new insight on alkali ion effects on a variety of adsorbates relevant to the CO 2 and CO reduction reactions by describing specific local ion–adsorbate interactions, systematic changes in adsorbate–electrolyte interactions induced by explicit surface charge, and comparisons of the calculated effects on binding energies to simple electrostatic field–adsorbate models to explain trends among various adsorbates and at varying surface charge densities and supercell configurations.

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

Cryogenic “Iodide-Tagging” Photoelectron Spectroscopy: A Sensitive Probe for Specific Binding Sites of Amino Acids

This work showcases cryogenic and temperature-dependent “iodide-tagging” photoelectron spectroscopy to probe specific binding sites of amino acids using the glycine-iodide complex (Gly?I-) as a case study. Multiple Gly?I- isomers were generated from ambient electrospray ionization and kinetically isolated in a cryogenic ion trap. These structures were characterized with temperature-dependent “iodide-tagging” negative ion photoelectron spectroscopy (NIPES) where iodide was used as the “messenger” to interpret electronic energetics and structural information of various Gly?I- isomers. Accompanied by theoretical computations and Franck-Condon simulations, a total of five cluster structures have been identified along with their various binding motifs. This work demonstrates that “iodide-tagging” NIPES is a powerful general means for probing specific binding interactions in biological molecules of interest.

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

Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding

Inosine 5′-monophosphate dehydrogenase (IMPDH) is a promising antibiotic target. This enzyme catalyzes the NAD-dependent oxidation of inosine 5′-monophosphate (IMP) to xanthosine 5′-monophosphate (XMP), which is the rate-limiting step in guanine nucleotide biosynthesis. Bacterial IMPDH-specific inhibitors have been developed that bind to the NAD + site. These inhibitors display varied affinities to different bacterial IMPDHs that are not easily rationalized by X-ray crystal structures of enzyme–inhibitor complexes. Inspection of X-ray crystal structures of 25 enzyme–inhibitor complexes, including 10 newly described, suggested that a mobile active site flap may be a structural determinant of inhibitor potency. Saturation transfer difference NMR experiments also suggested that the flap may contact the inhibitors to varying extents in different IMPDHs. Flap residue Leu413 contacted some inhibitors but was not structured in the crystal structures of other inhibitor complexes. The substitution of Leu413 with Phe or Ala in Bacillus anthracis IMPDH had inhibitor-selective effects, suggesting residue 413 could be a structural determinant of affinity. Curiously, the Ala substitution increased the potency of most inhibitors, even those that contacted Leu413 in the crystal structures. Presteady-state and steady-state kinetics experiments showed that the Leu413Ala substitution had comparable effects on inhibitor binding to the noncovalent E·IMP complex and the covalent intermediate E-XMP*, suggesting that the flap had similar interactions in both complexes. These results demonstrate that contacts do not necessarily indicate favorable interactions, and poorly structured mobile regions should not be discounted when assessing binding determinants.

Conformation↗
DOE OSTI2023

Impact of Hydrogen Bonds on CO 2 Binding in Eutectic Solvents: An Experimental and Computational Study toward Sorbent Design for CO 2 Capture

Choline-based amino acid ionic liquids with anions glycinate, β-alaninate, phenylalaninate, and prolinate were synthesized and mixed with ethylene glycol to form lower-viscosity benign eutectic solvents for CO 2 capture. The highest capacity measured was 0.7 moles of CO 2 per mole of ionic liquid (2 moles CO 2 per kg solvent) for a 1 to 2 mole ratio mixture of choline prolinate to ethylene glycol at 1 bar of CO 2 and 25 °C. Under 5000 ppm of CO 2 , half of this capacity was realized. Here, through a combined study of quantitative 13 C NMR spectroscopy, molecular dynamics simulations and density functional theory calculations, we show that hydrogen bonding in the eutectic solvent prevents proton-transfer between prolinate anions upon CO 2 absorption, which occurs in the absence of ethylene glycol and deactivates binding sites. Blocking this proton transfer leads to a higher binding capacity compared to neat choline prolinate. This work demonstrates the impact of hydrogen bonding on the CO 2 binding mechanism and energetics, as well as physical and thermal properties in eutectic solvents, thus addressing an unmet need and informing future studies on the development of benign sorbents for capturing CO 2 from dilute streams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗