Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “binding affinities”

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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation

The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid–liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1–chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.

3D genomics↗
DOE OSTI2022

Therapeutic Targeting of LIF Overcomes Macrophage-mediated Immunosuppression of the Local Tumor Microenvironment

Abstract Purpose: Leukemia inhibitory factor (LIF) is a multifunctional cytokine with numerous reported roles in cancer and is thought to drive tumor development and progression. Characterization of LIF and clinical-stage LIF inhibitors would increase our understanding of LIF as a therapeutic target. Experimental Design: We first tested the association of LIF expression with transcript signatures representing multiple processes regulating tumor development and progression. Next, we developed MSC-1, a high-affinity therapeutic antibody that potently inhibits LIF signaling and tested it in immune competent animal models of cancer. Results: LIF was associated with signatures of tumor-associated macrophages (TAM) across 7,769 tumor samples spanning 22 solid tumor indications. In human tumors, LIF receptor was highly expressed within the macrophage compartment and LIF treatment drove macrophages to acquire immunosuppressive capacity. MSC-1 potently inhibited LIF signaling by binding an epitope that overlaps with the gp130 receptor binding site on LIF. MSC-1 showed monotherapy efficacy in vivo and drove TAMs to acquire antitumor and proinflammatory function in syngeneic colon cancer mouse models. Combining MSC-1 with anti-PD1 leads to strong antitumor response and a long-term tumor-free survival in a significant proportion of treated mice. Conclusions: Overall, our findings highlight LIF as a therapeutic target for cancer immunotherapy.

Oncology↗
DOE OSTI2023

Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin‐Deubiquitylating Enzyme Interactions

Abstract Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C‐terminal electrophiles (Ub−E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub−Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p‐benzoyl‐L‐phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub‐based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine‐based chemistries.

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

Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein

IGHV3-33 -encoded antibodies are prevalent in the human humoral response against the Plasmodium falciparum circumsporozoite protein (PfCSP). Among VH3-33 antibodies, cross-reactivity between PfCSP major repeat (NANP), minor (NVDP), and junctional (NPDP) motifs is associated with high affinity and potent parasite inhibition. However, the molecular basis of antibody cross-reactivity and the relationship with efficacy remain unresolved. Here, we perform an extensive structure-function characterization of 12 VH3-33 anti-PfCSP monoclonal antibodies (mAbs) with varying degrees of cross-reactivity induced by immunization of mice expressing a human immunoglobulin gene repertoire. We identify residues in the antibody paratope that mediate cross-reactive binding and delineate four distinct epitope conformations induced by antibody binding, with one consistently associated with high protective efficacy and another that confers comparably potent inhibition of parasite liver invasion. Our data show a link between molecular features of cross-reactive VH3-33 mAb binding to PfCSP and mAb potency, relevant for the development of antibody-based interventions against malaria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Low-Energy Electron Elastic Total Cross Sections for Ho, Er, Tm, Yb, Lu, and Hf Atoms

The robust Regge-pole methodology wherein is fully embedded the essential electron-electron correlation effects and the vital core polarization interaction has been used to explore negative ion formation in the large lanthanide Ho, Er, Tm, Yb, Lu, and Hf atoms through the electron elastic total cross sections (TCSs) calculations. These TCSs are characterized generally by dramatically sharp resonances manifesting ground, metastable, and excited negative ion formation during the collisions, Ramsauer-Townsend minima, and shape resonances. The novelty and generality of the Regge-pole approach is in the extraction of the negative ion binding energies (BEs) of complex heavy systems from the calculated electron TCSs. The extracted anionic BEs from the ground state TCSs for Ho, Er, Tm, Yb, Lu, and Hf atoms are 3.51 eV, 3.53 eV, 3.36 eV, 3.49 eV, 4.09 eV and 1.68 eV, respectively. The TCSs are presented and the extracted from the ground; metastable and excited anionic states BEs are compared with the available measured and/or calculated electron affinities. We conclude with a remark on the existing inconsistencies in the meaning of the electron affinity among the various measurements and/or calculations in the investigated atoms and make a recommendation to resolve the ambiguity.

Felfli, Zineb↗
DOE OSTI2020

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface

The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of “undruggability” for an intracellular target. Structural studies reveal extensive protein–WDB002 and protein–protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise “undruggable” targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Diethylenetriamine-functionalized graphene oxide: Insights into ion adsorption and applications in rare earth element separation

The growing demand for critical minerals and materials requires atom- and energy-efficient, selective separations to overcome the challenges posed by the similar chemical and physical properties of the rare earth elements (REEs) and their low concentrations in unconventional domestic feedstocks. Here, in this study, we developed diethylenetriamine-functionalized graphene oxide (DETA-GO) as a membrane material for REE adsorption and separation. Synthesis conditions were optimized to maximize nitrogen incorporation while also preserving GO dispersibility for facile membrane fabrication. We investigated the mechanism of amine functionalization, the nitrogen-bonding configurations, the organization of the interlayer transport channels, and the resulting effects on ion and water transport for REE separations. Neat-GO and DETA-GO multilayer laminate membranes were fabricated by vacuum filtration onto polymer supports. To investigate the effects of amine functionalization, the membranes were characterized using scanning electron microscopy, Raman, Fourier transform infrared, and X-ray photoelectron spectroscopy, as well as grazing-incidence X-ray diffraction measurements. Ion permeation experiments with representative lanthanum (La 3+ ) and ytterbium (Yb 3+ ) solutions revealed enhanced ion adsorption and water transport through DETA-GO membranes compared to neat-GO. The strong affinity of the membranes for multivalent REEs was also validated with conductivity and inductively coupled plasma mass spectrometry measurements. Atomistic insight into the role of amine functionalization in modulating nanochannel architecture and long-term stability, optimizing adsorption sites, and regulating REE and water transport was obtained using classical molecular dynamics simulations. Collectively, our joint experimental and theoretical study demonstrates the potential of DETA-GO membranes for selective REE separations, offering insights into ion-binding mechanisms, water-transport properties, and nanochannel optimization for the recovery of critical materials from aqueous feedstocks.

Adsorbent↗
DOE OSTI2020

Capture and release of acid gasses using tunable organic solvents with aminopyridine

A class of water lean, organic solvents that can bind with various acid gasses to form acid gas bound molecules having a high degree of intramolecular hydrogen bonding which enables their use as regenerable solvents for acid gas capture. Unlike the other devices described in the prior art, the present invention takes advantage of shortened distances between the portions of the molecule that form hydrogen bonds within the structures when loaded with an acid gas so as to create a molecule with a higher internal bonding affinity and a reduced proclivity for agglomeration with other molecules.

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

Capture and release of acid gasses using tunable organic solvents with aminopyridine

A class of water lean, organic solvents that can bind with various acid gasses to form acid gas bound molecules having a high degree of intramolecular hydrogen bonding which enables their use as regenerable solvents for acid gas capture. Unlike the other devices described in the prior art, the present invention takes advantage of shortened distances between the portions of the molecule that form hydrogen bonds within the structures when loaded with an acid gas so as to create a molecule with a higher internal bonding affinity and a reduced proclivity for agglomeration with other molecules.

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

Spectroscopic evidence for intact carbonic acid stabilized by halide anions in the gas phase

Here we show elusive carbonic acid being effectively stabilized in the gas phase by interacting with halide anions X – (X = F, Cl, Br, and I). The formed H 2 CO 3 ·X – complexes, characterized by negative ion photoelectron spectroscopy and ab initio calculations, all contain intact trans – trans carbonic acid binding onto the respective halide via two identical strong ionic O–H...X – hydrogen bonds. For X = Cl, Br, and I, the complex spectra exhibit the corresponding X – signature by simply shifting to the higher binding energy side, while an extremely 2 eV wide broader band is observed for X = F. This spectroscopic evidence indicates that an excess electron is removed from each halide in the former case, while a proton is transferred from carbonic acid to fluoride upon electron detachment for the latter. The above H 2 CO 3 ·X – structures as well as those of the previously studied H 2 SO 4 ·X – along the homologous halogen series cannot be explained using the proton affinity (PA) argument. Instead, a qualitative correlation is found between these structural motifs and the constituent acid p K a values, strongly suggesting that p K a is a more suitable factor to predict correct acid–base chemistry between these diprotic oxyacids and halides.

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

Coupling of Ca 2+ and voltage activation in BK channels through the αB helix/voltage sensor interface

Large-conductance Ca 2+ and voltage-activated K + (BK) channels control membrane excitability in many cell types. BK channels are tetrameric. Each subunit is composed of a voltage sensor domain (VSD), a central pore-gate domain, and a large cytoplasmic domain (CTD) that contains the Ca 2+ sensors. While it is known that BK channels are activated by voltage and Ca 2+ , and that voltage and Ca 2+ activations interact, less is known about the mechanisms involved. In this work we explore these mechanisms by examining the gating contribution of an interface formed between the VSDs and the αB helices located at the top of the CTDs. Proline mutations in the αB helix greatly decreased voltage activation while having negligible effects on gating currents. Analysis with the Horrigan, Cui, and Aldrich model indicated a decreased coupling between voltage sensors and pore gate. Proline mutations decreased Ca 2+ activation for both Ca 2+ bowl and RCK1 Ca 2+ sites, suggesting that both high-affinity Ca 2+ sites transduce their effect, at least in part, through the αB helix. Mg 2+ activation also decreased. The crystal structure of the CTD with proline mutation L390P showed a flattening of the first helical turn in the αB helix compared to wild type, without other notable differences in the CTD, indicating that structural changes from the mutation were confined to the αB helix. These findings indicate that an intact αB helix/VSD interface is required for effective coupling of Ca 2+ binding and voltage depolarization to pore opening and that shared Ca 2+ and voltage transduction pathways involving the αB helix may be involved.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV

The design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications.

Conti, Simone (ORCID:000000017986567X)↗
DOE OSTI2025

Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal SARS-CoV-2 antagonist

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. We describe the development of a biologic that takes advantage of the proximity of the N-terminus of bound ACE2 to the three-fold symmetry axis of the spike protein to create an ultrapotent, trivalent ACE2 entry antagonist. Distinct disulfide bonds were added to enhance serum stability and a single point mutation was introduced to eliminate enzymatic activity. Through surface plasmon resonance, pseudovirus neutralization assays, and single-particle cryo-electron microscopy, we show this antagonist binds to and inhibits SARS-CoV-2 variants. We further show the antagonist binds to and inhibits a 2003 SARS-CoV-1 strain. Collectively, structural insight has allowed us to design a universal trivalent antagonist against all variants of SARS-CoV-2 tested, suggesting it will be active against the emergence of future mutants.

Gonzales, Juliet (ORCID:0000000327219566)↗
DOE OSTI2026

Cryo-electron microscopy structure of a zinc uptake ABC transporter

Zn2+ is an essential micronutrient required for many biological processes. Microorganisms employ high-affinity Zn2+ ABC transporters to take up zinc from the environment when it is scarce, yet the mechanism of zinc uptake and its regulation remain poorly understood. Here, we report the cryo-electron microscopy structure of the Zn2+ ABC transporter complex ZnuB-ZnuC from Escherichia coli. It contains two ZnuB transport and two ZnuC regulatory subunits. The ZnuB homodimer is in an outward-facing, closed conformation with a large hydrophilic cavity at the dimer interface. Each ZnuC subunit contains an N-terminal nucleotide-binding domain and a C-terminal zinc-sensing domain (ZSD). Zn2+ binding to the ZSD locks the transporter in a closed state, whereas under low-Zn2+ conditions, the disorder of ZSD permits ATP-driven zinc uptake. Zn2+ ABC transporters are ubiquitously utilized by pathogenic bacteria to compete with hosts for Zn2+. These findings reveal potential therapeutic targets for disrupting Zn2+ homeostasis in antibiotic-resistant pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Theoretical and Experimental Study of the Spectroscopy and Thermochemistry of UC +/0/–

A combination of high-level ab initio calculations and anion photoelectron detachment (PD) measurements is reported for the UC, UC – , and UC + molecules. To better compare the theoretical values with the experimental photoelectron spectrum (PES), a value of 1.493 eV for the adiabatic electron affinity (AEA) of UC was calculated at the Feller–Peterson–Dixon (FPD) level. The lowest vertical detachment energy (VDE) is predicted to be 1.500 eV compared to the experimental value of 1.487 ± 0.035 eV. A shoulder to lower energy in the experimental PD spectrum with the 355 nm laser can be assigned to a combination of low-lying excited states of UC – and excited vibrational states. The VDEs calculated for the low-lying excited electronic states of UC at the SO-CASPT2 level are consistent with the observed additional electron binding energies at 1.990, 2.112, 2.316, and 3.760 eV. Potential energy curves for the Ω states and the associated spectroscopic properties are also reported. Compared to UN and UN + , the bond dissociation energy (BDE) of UC (411.3 kJ/mol) is predicted to be considerably lower. The natural bond orbitals (NBO) calculations show that the UC 0/+/– molecules have a bond order of 2.5 with their ground-state configuration arising from changes in the oxidation state of the U atom in terms of the 7s orbital occupation: UC (5f 2 7s 1 ), UC – (5f 2 7s 2 ), and UC + (5f 2 7s 0 ). Furthermore, the behavior of the UN and UC sequence of molecules and anions differs from the corresponding sequences for UO and UF.

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

DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 M pro inhibitors

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed more than 4 million humans globally, but there is no bona fide Food and Drug Administration–approved drug-like molecule to impede the COVID-19 pandemic. The sluggish pace of traditional therapeutic discovery is poorly suited to producing targeted treatments against rapidly evolving viruses. Here, we used an affinity-based screen of 4 billion DNA-encoded molecules en masse to identify a potent class of virus-specific inhibitors of the SARS-CoV-2 main protease (M pro ) without extensive and time-consuming medicinal chemistry. CDD-1714, the initial three-building-block screening hit (molecular weight [MW] = 542.5 g/mol), was a potent inhibitor (inhibition constant [K i ] = 20 nM). CDD-1713, a smaller two-building-block analog (MW = 353.3 g/mol) of CDD-1714, is a reversible covalent inhibitor of M pro (K i = 45 nM) that binds in the protease pocket, has specificity over human proteases, and shows in vitro efficacy in a SARS-CoV-2 infectivity model. Subsequently, key regions of CDD-1713 that were necessary for inhibitory activity were identified and a potent (K i = 37 nM), smaller (MW = 323.4 g/mol), and metabolically more stable analog (CDD-1976) was generated. Thus, screening of DNA-encoded chemical libraries can accelerate the discovery of efficacious drug-like inhibitors of emerging viral disease targets.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Selective Biosorption of Valuable Rare Earth Elements Among Co-Occurring Lanthanides

To meet the increasing demand for rare earth elements (REEs) essential for low carbon-intensity energy technologies, new methods are needed for selective REE extraction from unconventional resources. Only a few REEs have significant economic value, but isolation of target rare earths from co-occurring lanthanides is challenging due to their similar chemical behavior. We present a novel approach to enhance separation of specific REEs from lanthanide mixtures. Escherichia coli cells engineered with lanthanide binding tags (LBTs) were immobilized in nonadsorbing, permeable polyethylene glycol diacrylate beads and packed into continuous flow, fixed-bed columns. Breakthrough of 15 rare earths in the +3 oxidation state resulted in notable differences in adsorption selectivity, with greatest separation between europium (Eu) and lanthanum (La) due to competitive displacement. REE adsorption onto fixed-bed columns was predicted by coupling a surface complexation model to a calibrated one-dimensional dual porosity transport model that accounts for interbead advective and intrabead diffusive transport. A tradeoff between high-abundance, low-affinity native carboxyl sites and low-abundance, high-affinity engineered LBT sites dictates process recovery efficiency and selectivity. Key chemical and operational parameters are identified to maximize selective extraction of high-value lanthanides, achieving a threefold enhancement of Eu recovery relative to La in a mixed REE solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗