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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Identification of Amino Acids that Account for Long-Range Interactions in Two Triosephosphate Isomerases from Pathogenic Trypanosomes

For a better comprehension of the structure-function relationship in proteins it is necessary to identify the amino acids that are relevant for measurable protein functions. Because of the numerous contacts that amino acids establish within proteins and the cooperative nature of their interactions, it is difficult to achieve this goal. Thus, the study of protein-ligand interactions is usually focused on local environmental structural differences. Here, using a pair of triosephosphate isomerase enzymes with extremely high homology from two different organisms, we demonstrate that the control of a seventy-fold difference in reactivity of the interface cysteine is located in several amino acids from two structurally unrelated regions that do not contact the cysteine sensitive to the sulfhydryl reagent methylmethane sulfonate, nor the residues in its immediate vicinity. The change in reactivity is due to an increase in the apparent pKa of the interface cysteine produced by the mutated residues. Our work, which involved grafting systematically portions of one protein into the other protein, revealed unsuspected and multisite long-range interactions that modulate the properties of the interface cysteines and has general implications for future studies on protein structure-function relationships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Higher-order interaction effects among operating conditions and feedstocks shape reactor microbiomes and fatty acid production profiles

Arrested anaerobic digestion (AAD) offers a promising route for producing fatty acids (FAs) from organic residues, yet optimal conditions for selectively generating medium-chain fatty acids (MCFAs) remain poorly defined. Here, we systematically evaluated the main and interaction effects of pH (5, 7, 9), feedstock (food waste, manure), temperature (35 and 45 °C), and inoculum source on microbiome composition and FA production. Anaerobic digester sludge and a novel bison rumen inoculum were compared. Significant higher-order interactions among operating parameters governed FA profiles and microbiome structure. Butyric acid production was driven by a three-way interaction among pH, feedstock, and temperature (p < 0.001), with maximum concentrations achieved in food waste reactors at pH 5.0 and 35 °C (1.2 ± 0.1 g L −1 with sludge and 1.1 ± 0.3 g L −1 with rumen). MCFA production exhibited significant four-way interactions (p < 0.1 to p < 0.001). At 45 °C and pH 5.0, inoculum source tuned MCFA selectivity: sludge favored pentanoic acid (0.4 ± 0.1 g L −1 ), whereas rumen favored hexanoic and heptanoic acids (up to 0.4 ± 0.2 g L −1 ). Manure reactors produced < 0.2 g L −1 MCFAs under all conditions. Genera, including Megasphaera, Prevotella, and Lactobacillus, were associated with production of specific MCFAs. PICRUSt2-based pathway predictions were consistent with MCFA production patterns and suggested a potential role for lactic acid–driven chain elongation pathways. This study provides insights into how interacting operating conditions shape AAD microbiomes, their FA profiles, and advances the trajectory of research aimed at engineering robust and controllable microbiomes for waste valorization.

09 BIOMASS FUELS↗
DOE OSTI2012

Gamow-Teller transitions from {sup 56}Ni

A new technique to measure (p,n) charge-exchange reactions in inverse kinematics at intermediate energies on unstable isotopes was successfully developed and used to study the {sup 56}Ni(p,n) reaction at 110 MeV/u. Gamow-Teller transition strengths from {sup 56}Ni to {sup 56}Cu were obtained and compared with shell-model predictions in the pf-shell using the KB3G and GXPF1A interactions. The calculations with the GXPF1A interaction reproduce the experimental GT strength distribution much better than the calculations that employed the KB3G interaction, indicating deficiencies in the spin-orbit and proton-neutron residual potentials for the latter. The results are important for improving the description of electron-capture rates on nuclei in the iron region, which are important for modeling the late evolution of core-collapse and thermonuclear supernovae.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Histone H4 Lys 20 methyltransferase SET8 promotes androgen receptor-mediated transcription activation in prostate cancer

Highlights: • Dihydrotestosterone stimulates H4K20me1 enrichment at the PSA promoter. • SET8 promotes AR-mediated transcription activation. • SET8 interacts with AR and promotes cell proliferation. - Abstract: Histone methylation status in different lysine residues has an important role in transcription regulation. The effect of H4K20 monomethylation (H4K20me1) on androgen receptor (AR)-mediated gene transcription remains unclear. Here we show that AR agonist stimulates the enrichment of H4K20me1 and SET8 at the promoter of AR target gene PSA in an AR dependent manner. Furthermore, SET8 is crucial for the transcription activation of PSA. Co-immunoprecipitation analyses demonstrate that SET8 interacts with AR. Therefore, we conclude that SET8 is involved in AR-mediated transcription activation, possibly through its interaction with AR and H4K20me1 modification.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Residual mean field model of valence quarks in the nucleon

Abstract We develop a non-perturbative model for valence parton distribution functions (PDFs) based on the mean field interactions of valence quarks in the nucleonic interior. The main motivation for the model is to obtain a mean field description of the valence quarks as a baseline to study the short range quark–quark interactions that generate the high x tail of PDFs. The model is based on the separation of the valence three-quark cluster and residual system in the nucleon. Then the nucleon structure function is calculated within the effective light-front diagrammatic approach introducing nonperturbative light-front valence quark and residual wave functions. Within the model a new relation is obtained between the position, $$x_p$$ x p , of the peak of $$xq_V(x)$$ x q V ( x ) distribution of the valence quark and the effective mass of the residual system, $$m_R$$ m R , in the form: $$x_{p} \approx {1\over 4} (1-{m_R\over m_N})$$ x p ≈ 1 4 ( 1 - m R m N ) at starting $$Q^2$$ Q 2 . This relation explains the difference in the peak positions for d- and u-quarks through the expected difference of residual masses for valence d- and u-quark distributions. The parameters of the model are fixed by fitting the calculated valence quark distributions to the phenomenological PDFs. This allowed us to estimate the overall mean field contribution in baryonic and momentum sum rules for valence d- and u-quarks. Finally, the evaluated parameters of the non-perturbative wave functions of valence 3q-cluster and residual system can be used in calculation of other quantities such as nucleon form factors, generalized partonic and transverse momentum distributions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa

Abstract Despite significant differences in size and formal charge, the aldehyde dehydrogenasePaPauC (PA5312) fromPseudomonas aeruginosaPAO1 efficiently catalyzes the NAD + ‐dependent oxidation of the aminoaldehydes formed in polyamines degradation. We report here thatPaPauC also oxidizes 4‐guanidinebutyraldehyde, formed in one arginine degradation pathway, trimethylaminobutyraldehyde, of unknown metabolic origin, and indole‐3‐acetaldehyde, a precursor of the plant growth‐promoting hormone indoleacetic acid.PaPauC has been proposed as a potential target for combatingP. aeruginosa. However, understanding its structure–function relationships, crucial for developing specific inhibitors, is lacking. Using X‐ray crystallography, we identified the structural characteristics that determinePaPauC broad aldehyde specificity: a spacious aldehyde‐entrance tunnel and six active‐site residues. Docking simulations, site‐directed mutagenesis, and kinetic analyses support the interactions of Lys479 with glutamylated aminoaldehydes; Phe169, Trp176, and Phe467 with amino and guanidinium groups through cation–π interactions and with the indole group via NH–π and CH–π interactions; Asp459 with amino and indole groups; and Thr303 with amide and guanidinium groups. Exploiting the distinctive structural features of thePaPauC active site could aid in developing specific inhibitors to combatP. aeruginosainfections in humans and animals, as well as in preventing its colonization of plants, which are abundantP. aeruginosareservoirs and, therefore, a significant source of human infections.

Biochemistry & Molecular Biology↗
DOE OSTI2018

Talin is a substrate for SUMOylation in migrating cancer cells

Highlights: • Talin is SUMOylated in cancer cells. • SUMOylation may regulate focal adhesion disassembly and cell migration. • SUMOylation may also regulate cleavage of talin. • Other focal adhesion proteins have been identified as potential SUMO targets including filamin-A and vinculin. Focal adhesions (FAs) play an important role in cancer cell migration and metastasis by linking the actin cytoskeleton to the extracellular matrix, allowing the cell to generate traction. SUMOylation is a post-translational modification of proteins on lysine residues that can affect protein localisation, turnover and protein-protein interactions. In this study, we demonstrate that talin, a key component of FAs, can be post-translationally modified by SUMOylation in MDA-MB-231 breast cancer cells and U2OS osteosarcoma cells. Furthermore we demonstrate that SUMOylation regulates the dynamic activities of FAs including their number, size and turnover rate. Inhibiting SUMOylation significantly reduced the speed of cell migration. The identification of talin as a SUMO target provides insight into the mechanisms regulating focal adhesion formation and turnover and potentially identifies a novel mechanism underlying cell migration.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48

Despite the advances in β-lactamase inhibitor development, limited options exist for the class D carbapenemase known as OXA-48. OXA-48 is one of the most prevalent carbapenemases in carbapenem-resistant Enterobacteriaceae infections and is not susceptible to most available β-lactamase inhibitors. Here, we screened various low-molecular-weight compounds (fragments) against OXA-48 to identify functional scaffolds for inhibitor development. Several biphenyl-, naphthalene-, fluorene-, anthraquinone-, and azobenzene-based compounds were found to inhibit OXA-48 with low micromolar potency despite their small size. Co-crystal structures of OXA-48 with several of these compounds revealed key interactions with the carboxylate-binding pocket, Arg214, and various hydrophobic residues of β-lactamase that can be exploited in future inhibitor development. A number of the low-micromolar-potency inhibitors, across different scaffolds, synergize with ampicillin to kill Escherichia coli expressing OXA-48, albeit at high concentrations of the respective inhibitors. Additionally, several compounds demonstrated micromolar potency toward the OXA-24 and OXA-58 class D carbapenemases that are prevalent in Acinetobacter baumannii . In conclusion, this work provides foundational information on a variety of chemical scaffolds that can guide the design of effective OXA-48 inhibitors that maintain efficacy as well as potency toward other major class D carbapenemases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

An investigation of low temperature electronic phase arrest in Sm{sub 0.55}Sr{sub 0.45}MnO{sub 3} phase separated manganite

The temperature dependence of electronic-transport and magneto-transport of polycrystalline Sm{sub 0.55}Sr{sub 0.45}MnO{sub 3} manganite at low temperatures has been investigated in detail. The low temperature resistivity data show a distinct minimum in the resistivity versus temperature plots for all fields. The low temperature resistivity upturn below this minimum has been fitted to an expression, which includes three terms, namely, residual resistivity, inelastic scattering, and electron-electron (e-e) interaction or Kondo effects. It has been found that the dominating mechanism is e-e interaction. The resistivity of the sample shows strong dependence on the magnetic field–temperature history. The electronic-transport property clearly confirms that the electronic phase of the sample gets arrested to a low resistive state during field cooling and cannot return to its original state even after the magnetic field is removed. The magnetoresistance of the sample also shows a strong irreversibility with respect to the sweeping of the magnetic field between its highest positive and negative values. Moreover, the resistivity of the sample is found to be time dependent. All the observed phenomena have been explained through the phase separation scenario and kinetic arrest of electronic phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

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

Local and global structural drivers for the photoactivation of the orange carotenoid protein

Significance The orange carotenoid protein (OCP) is critical for the antenna-associated energy-dissipation mechanism of cyanobacteria under high light conditions. We show that light activation causes a global conformation change, the complete separation of the two domains of the OCP. Such a conformational change has been postulated to be a prerequisite for interaction with the antenna. We also identify local structural changes in residue solvent accessibility and roles for structural water molecules in activation of the OCP. By combining small-angle scattering, hydrogen-deuterium exchange, and X-ray hydroxyl radical footprinting studies, we were able to construct a model of the structural changes during the activation of the OCP with an unprecedented level of detail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Crystal structure of MICU2 and comparison with MICU1 reveal insights into the uniporter gating mechanism

The mitochondrial uniporter is a Ca 2+ -channel complex resident within the organelle’s inner membrane. In mammalian cells the uniporter’s activity is regulated by Ca 2+ due to concerted action of MICU1 and MICU2, two paralogous, but functionally distinct, EF-hand Ca 2+ -binding proteins. In this paper, we present the X-ray structure of the apo form of Mus musculus MICU2 at 2.5-Å resolution. The core structure of MICU2 is very similar to that of MICU1. It consists of two lobes, each containing one canonical Ca 2+ -binding EF-hand (EF1, EF4) and one structural EF-hand (EF2, EF3). Two molecules of MICU2 form a symmetrical dimer stabilized by highly conserved hydrophobic contacts between exposed residues of EF1 of one monomer and EF3 of another. Similar interactions stabilize MICU1 dimers, allowing exchange between homo- and heterodimers. The tight EF1–EF3 interface likely accounts for the structural and functional coupling between the Ca 2+ -binding sites in MICU1, MICU2, and their complex that leads to the previously reported Ca 2+ -binding cooperativity and dominant negative effect of mutation of the Ca 2+ -binding sites in either protein. The N- and C-terminal segments of the two proteins are distinctly different. In MICU2 the C-terminal helix is significantly longer than in MICU1, and it adopts a more rigid structure. MICU2’s C-terminal helix is dispensable in vitro for its interaction with MICU1 but required for MICU2’s function in cells. We propose that in the MICU1–MICU2 oligomeric complex the C-terminal helices of both proteins form a central semiautonomous assembly which contributes to the gating mechanism of the uniporter.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A two-component protein condensate of the EGFR cytoplasmic tail and Grb2 regulates Ras activation by SOS at the membrane

We reconstitute a phosphotyrosine-mediated protein condensation phase transition of the ~200 residue cytoplasmic tail of the epidermal growth factor receptor (EGFR) and the adaptor protein, Grb2, on a membrane surface. The phase transition depends on phosphorylation of the EGFR tail, which recruits Grb2, and crosslinking through a Grb2-Grb2 binding interface. The Grb2 Y160 residue plays a structurally critical role in the Grb2-Grb2 interaction, and phosphorylation or mutation of Y160 prevents EGFR:Grb2 condensation. By extending the reconstitution experiment to include the guanine nucleotide exchange factor, SOS, and its substrate Ras, we further find that the condensation state of the EGFR tail controls the ability of SOS, recruited via Grb2, to activate Ras. These results identify an EGFR:Grb2 protein condensation phase transition as a regulator of signal propagation from EGFR to the MAPK pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus , Sulfolobus tokodaii and Methanocaldococcus jannaschii

The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus , Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus , two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the interaction site with PurL and PurQ, the other subunits of the formylglycinamide ribonucleotide amidotransferase. Molecular-dynamics simulations of the PurS dimer as well as a model of the complex of the PurS dimer, PurL and PurQ suggest that PurS plays some role in the catalysis of the enzyme by its bending motion.

Watanabe, Yuzo↗
DOE OSTI2012

Text Mining Improves Prediction of Protein Functional Sites

We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Cysteine Specific Targeting of the Functionally Distinct Peroxiredoxin and Glutaredoxin Proteins by the Investigational Disulfide BNP7787

Glutaredoxin (Grx), peroxiredoxin (Prx), and thioredoxin (Trx) are redoxin family proteins that catalyze different types of chemical reactions that impact cell growth and survival through functionally distinct intracellular pathways. Much research is focused on understanding the roles of these redoxin proteins in the development and/or progression of human diseases. Grx and Prx are overexpressed in human cancers, including human lung cancers. BNP7787 is a novel investigational agent that has been evaluated in previous clinical studies, including non-small cell lung cancer (NSCLC) studies. Herein, data from activity assays, mass spectrometry analyses, and X-ray crystallographic studies indicate that BNP7787 forms mixed disulfides with select cysteine residues on Grx and Prx and modulates their function. Studies of interactions between BNP7787 and Trx have been conducted and reported separately. Despite the fact that Trx, Grx, and Prx are functionally distinct proteins that impact oxidative stress, cell proliferation and disease processes through different intracellular pathways, BNP7787 can modify each protein and appears to modulate function through mechanisms that are unique to each target protein. Tumor cells are often genomically heterogeneous containing subpopulations of cancer cells that often express different tumor-promoting proteins or that have multiple dysregulated signaling pathways modulating cell proliferation and drug resistance. A multi-targeted agent that simultaneously modulates activity of proteins important in mediating cell proliferation by functionally distinct intracellular pathways could have many potentially useful therapeutic applications.

BNP7787↗
NASA NTRS1988

A unified process for systems identification based on performance assessment

Many modern spacecraft are complex multi-body dynamic systems where the bodies are connected by several active control systems for pointing and isolation. Mission requirements indicate that many structural modes and possibly some nonlinear effects will require characterization. Thus, even characterization at the subsystem level will become more difficult than usual. System level characterization difficulties will be compounded by the fact that only limited ground testing will be possible on the full up system, and flight testing will be restricted by an extremely limited measurements set. The object of the present discussion is the application of matrix majorant theory to the problem of assessing dynamic system performance when knowledge of the system is uncertain. We show how majorants provide an effective tool to relate required performance output to system identification test quality in terms of residual uncertainty in input-output relations, parameter values, nonlinearities, and interactions. The underlying machinery consists of the block-norm matrix which is a nonnegative matrix each of whose elements is the norm of a block of a suitably partitioned matrix. A matrix which bounds the block-norm matrix in the sense of nonnegative matrices, i.e., element by element is known as a majorant.

Hyland, C.↗