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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation

Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.

Science & Technology - Other Topics↗
DOE OSTI2022

An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking

β-Coronaviruses such as SARS-CoV-2 hijack coatomer protein-I (COPI) for spike protein retrograde trafficking to the progeny assembly site in endoplasmic reticulum-Golgi intermediate compartment (ERGIC). However, limited residue-level details are available into how the spike interacts with COPI. Here we identify an extended COPI binding motif in the spike that encompasses the canonical K-x-H dibasic sequence. This motif demonstrates selectivity for αCOPI subunit. Guided by an in silico analysis of dibasic motifs in the human proteome, we employ mutagenesis and binding assays to show that the spike motif terminal residues are critical modulators of complex dissociation, which is essential for spike release in ERGIC. αCOPI residues critical for spike motif binding are elucidated by mutagenesis and crystallography and found to be conserved in the zoonotic reservoirs, bats, pangolins, camels, and in humans. Collectively, our investigation on the spike motif identifies key COPI binding determinants with implications for retrograde trafficking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Relative binding affinities of monolignols to horseradish peroxidase

Monolignol binding to the peroxidase active site is the first step in lignin polymerization in plant cell walls. Using molecular dynamics, docking, and free energy perturbation calculations, we investigate the binding of monolignols to horseradish peroxidase C. Our results suggest that p-coumaryl alcohol has the strongest binding affinity followed by sinapyl and coniferyl alcohol. Stacking interactions between the monolignol aromatic rings and nearby phenylalanine residues play an important role in determining the calculated relative binding affinities. p-Coumaryl and coniferyl alcohols bind in a pose productive for reaction in which a direct H-bond is formed between the phenolic –OH group and a water molecule (W2) that may facilitate proton transfer during oxidation. In contrast, in the case of sinapyl alcohol there is no such direct interaction, the phenolic –OH group instead interacting with Pro139. Furthermore, since proton and electron transfer is the rate-limiting step in monolignol oxidation by peroxidase, the binding pose (and thus the formation of near attack conformation) appears to play a more important role than the overall binding affinity in determining the oxidation rate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex

Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ~150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. Finally, the Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein–Protein Interaction in Solution and Determination of Binding Energy Hot Spots

Mobilization of iron stored in the interior cavity of BfrB requires electron transfer from the [2Fe–2S] cluster in Bfd to the core iron in BfrB. A crystal structure of the Pseudomonas aeruginosa BfrB:Bfd complex revealed that BfrB can bind up to 12 Bfd molecules at 12 structurally identical binding sites, placing the [2Fe–2S] cluster of each Bfd immediately above a heme group in BfrB. We report here a study aimed at characterizing the strength of the P. aeruginosa BfrB:Bfd association using surface plasmon resonance and isothermal titration calorimetry as well as determining the binding energy hot spots at the protein–protein interaction interface. The results show that the 12 Bfd-binding sites on BfrB are equivalent and independent and that the protein–protein association at each of these sites is driven entropically and is characterized by a dissociation constant ( K d ) of approximately 3 μM. Determination of the binding energy hot spots was carried out by replacing certain residues that comprise the protein–protein interface with alanine and by evaluating the effect of the mutation on K d and on the efficiency of core iron mobilization from BfrB. The results identified hot spot residues in both proteins [L B 68 , E A 81 , and E A 85 in BfrB (superscript for residue number and subscript for chain) and Y 2 and L 5 in Bfd] that network at the interface to produce a highly complementary hot region for the interaction. The hot spot residues are conserved in the amino acid sequences of Bfr and Bfd proteins from a number of Gram-negative pathogens, indicating that the BfrB:Bfd interaction is of widespread significance in bacterial iron metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ruthenium/Carbon Nanocomposites for Efficient Hydrogen Electrocatalysis: Impacts of Halide Residues

Ruthenium has emerged as a promising substitute for platinum toward the hydrogen evolution/oxidation reaction (HER/HOR). Herein, ruthenium/carbon composites are prepared by magnetic induction heating (300 A, 10 s) of RuCl3, RuBr3 or RuI3 loaded on hollow N-doped carbon cages (HNC). The HNC-RuCl3-300A sample consists of Ru nanoparticles (dia. 1.96 nm) and abundant Cl residues. HNC-RuBr3-300A possesses a larger nanoparticle size (≈19.36 nm) and lower content of Br residues. HNC-RuI3-300A contains only bulk-like Ru agglomerates with a minimal amount of I residues, due to reduced Ru-halide bonding interactions. Among these, HNC-RuCl3-300A exhibits the best HER activity in alkaline media, with a low overpotential of only -26 mV to reach 10 mA cm-2, even outperforming Pt/C, and can be used as the cathode catalyst for anion exchange membrane water electrolyzer (along with commercial RuO2 as the anode catalyst), producing 0.5 A cm- 2 at 1.88 V for up to 100 h, a performance markedly better than that with Pt/C. HNC-RuCl3-300A also exhibits the best HOR activity, with a half-wave potential (+18 mV) even lower than that of Pt/C (+35 mV). These activities are ascribed to the combined contributions of small Ru nanoparticles and Ru-to-halide charge transfer that weaken H adsorption.

Yu, Bingzhe↗
DOE OSTI2020

The cosmological bootstrap: inflationary correlators from symmetries and singularities

Scattering amplitudes at weak coupling are highly constrained by Lorentz invariance, locality and unitarity, and depend on model details only through coupling constants and the particle content of the theory. For example, four-particle amplitudes are analytic for contact interactions and have simple poles with appropriately positive residues for tree-level exchange. In this paper, we develop an understanding of inflationary correlators which parallels that of flat-space scattering amplitudes. Specifically, we study slow-roll inflation with weak couplings to extra massive particles, for which all correlation functions are controlled by an approximate conformal symmetry on the boundary of the spacetime. After systematically classifying all possible contact terms in de Sitter space, we derive an analytic expression for the four-point function of conformally coupled scalars mediated by the tree-level exchange of massive scalars. Conformal symmetry implies that the correlator satisfies a pair of differential equations with respect to spatial momenta, encoding bulk time evolution in purely boundary terms. The absence of unphysical singularities (and the correct normalization of physical ones) completely fixes this correlator. Moreover, a “spin-raising” operator relates it to the correlators associated with the exchange of particles with spin, while “weight-shifting” operators map it to the four-point function of massless scalars. We explain how these de Sitter four-point functions can be perturbed to obtain inflationary three-point functions. Using our formalism, we reproduce many classic results in the literature, such as the three-point function of slow-roll inflation, and provide a complete classification of all inflationary three- and four-point functions arising from weakly broken conformal symmetry. Remarkably, the inflationary bispectrum associated with the exchange of particles with arbitrary spin is completely characterized by the soft limit of the simplest scalar-exchange four-point function of conformally coupled scalars and a series of contact terms. Finally, we demonstrate that the inflationary correlators contain flat-space scattering amplitudes via a suitable analytic continuation of the external momenta, which can also be directly connected with the signals for particle production seen in the squeezed limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Mechanistic insights into mode of action of potent natural antagonists of BACE-1 for checking Alzheimer’s plaque pathology

Highlights: •Accumulation of Aβ plaques is one of the major pathology associated with Alzheimer’s disease. •Inhibition of β-Secretase or BACE-1 offers a viable prospect to check the growth of these plaques. •A large virtual dataset of natural compounds was screened against BACE-1. •Top two hits were analyzed for thermodynamic and structural stability using MD simulations. •Their detailed binding mode of actions were elucidated. -- Abstract: Alzheimer’s is a neurodegenerative disorder resulting in memory loss and decline in cognitive abilities. Accumulation of extracellular beta amyloidal plaques is one of the major pathology associated with this disease. β-Secretase or BACE-1 performs the initial and rate limiting step of amyloidic pathway in which 37–43 amino acid long peptides are generated which aggregate to form plaques. Inhibition of this enzyme offers a viable prospect to check the growth of these plaques. Numerous efforts have been made in recent years for the generation of BACE-1 inhibitors but many of them failed during the preclinical or clinical trials due to drug related or drug induced toxicity. In the present work, we have used computational methods to screen a large dataset of natural compounds to search for small molecules having BACE-1 inhibitory activity with low toxicity to normal cells. Molecular dynamics simulations were performed to analyze molecular interactions between the screened compounds and the active residues of the enzyme. Herein, we report two natural compounds of inhibitory nature active against β-secretase enzyme of amyloidic pathway and are potent lead molecules against Alzheimer’s disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Towards First Principles-Based Prediction of Highly Accurate Electrochemical Pourbaix Diagrams

Electrochemical potential/pH (Pourbaix) diagrams underpin many aqueous electrochemical processes and are central to the identification of stable phases of metals for processes ranging from electrocatalysis to corrosion. Even though standard DFT calculations are potentially powerful tools for the prediction of such diagrams, inherent errors in the description of transition metal (hydroxy)oxides, together with neglect of van der Waals interactions, have limited the reliability of such predictions for even the simplest pure metal bulk compounds, and corresponding predictions for more complex alloy or surface structures are even more challenging. In the present work, through synergistic use of a Hubbard U correction, a state-of-the-art dispersion correction, and a water-based bulk reference state for the calculations, these errors are systematically corrected. The approach describes the weak binding that occurs between hydroxyl-containing functional groups in certain compounds in Pourbaix diagrams, corrects for self-interaction errors in transition metal compounds, and reduces residual errors on oxygen atoms by preserving a consistent oxidation state between the reference state, water, and the relevant bulk phases. The strong performance is illustrated on a series of bulk transition metal (Mn, Fe, Co and Ni) hydroxides, oxyhydroxides, binary, and ternary oxides, where the corresponding thermodynamics of redox and (de)hydration are described with standard errors of 0.04 eV per (reaction) formula unit. The approach further preserves accurate descriptions of the overall thermodynamics of electrochemically-relevant bulk reactions, such as water formation, which is an essential condition for facilitating accurate analysis of reaction energies for electrochemical processes on surfaces. The overall generality and transferability of the scheme suggests that it may find useful application in the construction of a broad array of electrochemical phase diagrams, including both bulk Pourbaix diagrams and surface phase diagrams of interest for corrosion and electrocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

QM and QM/MM Studies of Uranyl Fluorides in the Gas and Aqueous Phases and in the Hydrophobic Cavities of Tetrabrachion

The structural properties and electronic structures of pentacoordinated uranyl complexes belonging to the [UO₂Fn(H₂O) 5-n ] 2-n series have been studied in the gas and aqueous phases using density functionals with relativistic pseudopotentials and all-electron basis sets in the gas-phase calculations in combination with COSMO in the aqueous phase. In addition, the conformational orientation and structural and electronic properties of [UO₂F₅]³¯ in the hydrophobic cavities of the right-handed coiled-coil (RHCC) protein of tetrabrachion have been determined using the hybrid QM/MM method. Although there is good agreement between the available experimental geometrical parameters and the values obtained in the aqueous phase using pseudopotentials or all-electron basis sets, variation of the uranyl U=O bond with the number of fluoride ligands is only truly captured after the inclusion of five water molecules in the second coordination sphere around the molecules. The docking procedure used in this work shows that there are only two possible orientations of the uranyl group of [UO₂F₅]³¯ embedded in the hydrophobic cavities of the RHCC protein. The two orientations are exclusively along the axes perpendicular to the protein axial channel with no possible orientation of the uranyl group along the axial channel because of both steric effects and interaction with the alkyl chain of the isoleucine residues pointing into the axial channel. In addition, the embedded complex is always positioned nearer to the isoleucine residues at the N-terminal ends of the hydrophobic cavities. Energy analysis, however, reveals that both conformations can only be observed in cavity 2, the largest hydrophobic cavity. The structural and electronic properties of the ligand embedded in this cavity are very similar to those of the gas-phase structure. A comparable study of [Pt(CN)₆]²¯ and the anticancer drug cisplatin, [PtCl₂(NH₃)₂], in cavity 2, revealed the existence of just two orientations for the former, similar to the uranyl complex, and multiple orientations for the latter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

The molecular basis of phosphite and hypophosphite recognition by ABC-transporters

Inorganic phosphate is the major bioavailable form of the essential nutrient phosphorus. Yet, the concentration of phosphate in most natural habitats is low enough to limit microbial growth. Under phosphate-depleted conditions some bacteria utilise phosphite and hypophosphite as alternative sources of phosphorus, but the molecular basis of reduced phosphorus acquisition from the environment is not fully understood. Here, we present crystal structures and ligand binding affinities of periplasmic binding proteins from bacterial phosphite and hypophosphite ATP-binding cassette transporters. We reveal that phosphite and hypophosphite specificity results from a combination of steric selection and the presence of a P-H…π interaction between the ligand and a conserved aromatic residue in the ligand-binding pocket. The characterisation of high affinity and specific transporters has implications for the marine phosphorus redox cycle, and might aid the use of phosphite as an alternative phosphorus source in biotechnological, industrial and agricultural applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Intra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding

PUF proteins are characterized by globular RNA-binding domains. They also interact with partner proteins that modulate their RNA-binding activities. Caenorhabditis elegans PUF protein fem-3 binding factor-2 (FBF-2) partners with intrinsically disordered Lateral Signaling Target-1 (LST-1) to regulate target mRNAs in germline stem cells. Here, we report that an intrinsically disordered region (IDR) at the C-terminus of FBF-2 autoinhibits its RNA-binding affinity by increasing the off rate for RNA binding. Moreover, the FBF-2 C-terminal region interacts with its globular RNA-binding domain at the same site where LST-1 binds. This intramolecular interaction restrains an electronegative cluster of amino acid residues near the 5' end of the bound RNA to inhibit RNA binding. LST-1 binding in place of the FBF-2 C-terminus therefore releases autoinhibition and increases RNA-binding affinity. This regulatory mechanism, driven by IDRs, provides a biochemical and biophysical explanation for the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Pressure tuned ferroelectric reentrance in nano-BaTiO{sub 3} ceramics

In nano-grain BaTiO{sub 3} ceramics, internal compressive stresses make the cubic phase more stable, while internal shear stresses stabilize rhombohedral and orthorhombic phases. The competition between internal compressive stresses and internal shear stresses gives a ferroelectric to paraelectric to ferroelectric reentrance phenomenon as a function of grain size. The pressure can be a tuning factor of reentrance behavior by controlling the interactions between external hydrostatic pressure and internal compressive stresses. These experimental phenomena can be well described by a modified Ginzburg-Landau-Devonshire thermodynamic theory.

36 MATERIALS SCIENCE↗
DOE OSTI2015

High field terahertz emission from relativistic laser-driven plasma wakefields

We propose a method to generate high field terahertz (THz) radiation with peak strength of GV/cm level in the THz frequency gap range of 1–10 THz using a relativistic laser interaction with a gaseous plasma target. Due to the effect of local pump depletion, an initially Gaussian laser pulse undergoes leading edge erosion and eventually evolves to a state with leading edge being step function. Interacting with such a pulse, electrons gain transverse residual momentum and excite net transverse currents modulated by the relativistic plasma frequency. These currents give rise to the low frequency THz emission. We demonstrate this process with one and two dimensional particle-in-cell simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Arabidopsis Receptor of Activated C Kinase1 Phosphorylation by WITH NO LYSINE8 KINASE

Receptor of activated C kinase1 (RACK1) is a versatile scaffold protein that binds to numerous proteins to regulate diverse cellular pathways in mammals. In Arabidopsis (Arabidopsis thaliana), RACK1 has been shown to regulate plant hormone signaling, stress responses, and multiple processes of growth and development. However, little is known about the molecular mechanism underlying these regulations. In this paper, we show that an atypical serine (Ser)/threonine (Thr) protein kinase, WITH NO LYSINE8 (WNK8), phosphorylates RACK1. WNK8 physically interacted with and phosphorylated RACK1 proteins at two residues: Ser-122 and Thr-162. Genetic epistasis analysis of rack1 wnk8 double mutants indicated that RACK1 acts downstream of WNK8 in the glucose responsiveness and flowering pathways. The phosphorylation-dead form, RACK1AS122A/T162A, but not the phosphomimetic form, RACK1AS122D/T162E, rescued the rack1a null mutant, implying that phosphorylation at Ser-122 and Thr-162 negatively regulates RACK1A function. The transcript of RACK1AS122D/T162E accumulated at similar levels as those of RACK1S122A/T162A. However, although the steady-state level of the RACK1AS122A/T162A protein was similar to wild-type RACK1A protein, the RACK1AS122D/T162E protein was nearly undetectable, suggesting that phosphorylation affects the stability of RACK1A proteins. In conclusion, these results suggest that RACK1 is phosphorylated by WNK8 and that phosphorylation negatively regulates RACK1 function by influencing its protein stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine

Human xenobiotic-metabolizing cytochrome P450 (CYP) enzymes can each bind and monooxygenate a diverse set of substrates, including drugs, often producing a variety of metabolites. Additionally, a single ligand can interact with multiple CYP enzymes, but often the protein structural similarities and differences that mediate such overlapping selectivity are not well understood. Even though the CYP superfamily has a highly canonical global protein fold, there are large variations in the active site size, topology, and conformational flexibility. We have determined how a related set of three human CYP enzymes bind and interact with a common inhibitor, the muscarinic receptor agonist drug pilocarpine. Pilocarpine binds and inhibits the hepatic CYP2A6 and respiratory CYP2A13 enzymes much more efficiently than the hepatic CYP2E1 enzyme. To elucidate key residues involved in pilocarpine binding, crystal structures of CYP2A6 (2.4 {angstrom}), CYP2A13 (3.0 {angstrom}), CYP2E1 (2.35 {angstrom}), and the CYP2A6 mutant enzyme, CYP2A6 I208S/I300F/G301A/S369G (2.1 {angstrom}) have been determined with pilocarpine in the active site. In all four structures, pilocarpine coordinates to the heme iron, but comparisons reveal how individual residues lining the active sites of these three distinct human enzymes interact differently with the inhibitor pilocarpine.

59 BASIC BIOLOGICAL SCIENCES↗