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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity

Inosine 5'-monophosphate dehydrogenase (IMPDH) is a promising target for the treatment of Cryptosporidium infections. Here, the structure of C. parvum IMPDH ( Cp IMPDH) in complex with inosine 5'-monophosphate (IMP) and P131, an inhibitor with in vivo anticryptosporidial activity, is reported. P131 contains two aromatic groups, one of which interacts with the hypoxanthine ring of IMP, while the second interacts with the aromatic ring of a tyrosine in the adjacent subunit. In addition, the amine and NO 2 moieties bind in hydrated cavities, forming water-mediated hydrogen bonds to the protein. The design of compounds to replace these water molecules is a new strategy for the further optimization of C. parvum inhibitors for both antiparasitic and antibacterial applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Inhibition of Pyruvate Kinase From Thermoanaerobacterium saccharolyticum by IMP Is Independent of the Extra-C Domain

The pyruvate kinase (PYK) isozyme from Thermoanaerobacterium saccharolyticum (TsPYK) has previously been used in metabolic engineering for improved ethanol production. This isozyme belongs to a subclass of PYK isozymes that include an extra C-domain. Like other isozymes that include this extra C-domain, we found that TsPYK is activated by AMP and ribose-5-phosphate (R5P). Our use of sugar-phosphate analogs generated a surprising result in that IMP and GMP are allosteric inhibitors (rather than activators) of TsPYK. We believe this to be the first report of any PYK isozyme being inhibited by IMP and GMP. A truncated protein that lacks the extra C-domain is also inhibited by IMP. A screen of several other bacterial PYK enzymes (include several that have the extra-C domain) indicates that the inhibition by IMP is specific to only a subset of those isozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The structural basis for RNA selectivity by the IMP family of RNA-binding proteins

The IGF2 mRNA-binding proteins (ZBP1/IMP1, IMP2, IMP3) are highly conserved post-transcriptional regulators of RNA stability, localization and translation. They play important roles in cell migration, neural development, metabolism and cancer cell survival. The knockout phenotypes of individual IMP proteins suggest that each family member regulates a unique pool of RNAs, yet evidence and an underlying mechanism for this is lacking. Here, we combine systematic evolution of ligands by exponential enrichment (SELEX) and NMR spectroscopy to demonstrate that the major RNA-binding domains of the two most distantly related IMPs (ZBP1 and IMP2) bind to different consensus sequences and regulate targets consistent with their knockout phenotypes and roles in disease. We find that the targeting specificity of each IMP is determined by few amino acids in their variable loops. As variable loops often differ amongst KH domain paralogs, we hypothesize that this is a general mechanism for evolving specificity and regulation of the transcriptome.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2015

A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD + , which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis , Campylobacter jejuni , and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD + and XMP/NAD + . In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD + -binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD + -binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Status of Mercury and Imp: Two Monte Carlo Transport Codes Developed Using Shared Infrastructure at Lawrence Livermore National Laboratory

The Monte Carlo Transport Project at Lawrence Livermore National Laboratory develops two Monte Carlo transport codes used in production by a sizable internal user community. Mercury is a Monte Carlo particle transport code used to model the interaction of neutrons, gammas, and light ions with a material. Imp is an implicit Monte Carlo thermal x-ray photon transport code used to model the interaction of x-ray photons with a material. This paper describes the two codes and highlights recent developments.

Pozulp, Michael↗
DOE OSTI2020

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Input-Output Model for MACCS Nuclear Accident Imp Acts Estimation

Since the original economic model for MACCS was developed, better quality economic data (as well as the tools to gather and process it) and better computational capabilities have become available. The update of the economic impacts component of the MACCS legacy model will provide improved estimates of business disruptions through the use of Input-Output based economic impact estimation. This paper presents an updated MACCS model, bases on Input-Output methodology, in which economic impacts are calculated using the Regional Economic Accounting analysis tool (REAcct) created at Sandia National Laboratories. This new GDP-based model allows quick and consistent estimation of gross domestic product (GDP) losses due to nuclear power plant accidents. This paper outlines the steps taken to combine the REAcct Input-Output-based model with the MACCS code, describes the GDP loss calculation, and discusses the parameters and modeling assumptions necessary for the estimation of long-term effects of nuclear power plant accidents.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2017

Nuclear import of Nkx2-2 is mediated by multiple pathways

Nkx2-2 homeoprotein is essential for the development of the central nervous system and pancreas. Although the nuclear localization signals of Nkx2-2 have been identified, the responsible transport receptor is still unknown. Here, we demonstrate that imp α1 not only interacts with Nkx2-2 but also transports it into the nucleus in vitro by acting together with imp β1. However, the nuclear import of Nkx2-2 in cells was not inhibited in response to knockdown expression of endogenous imp β1 or over-expression of Bimax2. Furthermore, imp β1 and imp 13, but not imp 4, directly interact with Nkx2-2 and are capable of transporting Nkx2-2 in an in vitro import assay. By GST pull-down assay, we demonstrate that mutation of NLS1 or NLS2 has no effect on interaction with imp α1 or imp 13, but significantly reduced binding to imp β1. Thus, the nuclear import of Nkx2-2 is mediated not only by the classical import pathway but also directly by imp β1 or imp 13.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Intermediate Molecular Phenotypes to Identify Genetic Markers of Anthracycline-Induced Cardiotoxicity Risk

Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex trait with a polygenic component that is mainly unidentified. We propose that levels of intermediate molecular phenotypes (IMPs) in the myocardium associated with histopathological damage could explain CDA susceptibility, so variants of genes encoding these IMPs could identify patients susceptible to this complication. Thus, a genetically heterogeneous cohort of mice (n = 165) generated by backcrossing were treated with doxorubicin and docetaxel. We quantified heart fibrosis using an Ariol slide scanner and intramyocardial levels of IMPs using multiplex bead arrays and QPCR. We identified quantitative trait loci linked to IMPs (ipQTLs) and cdaQTLs via linkage analysis. In three cancer patient cohorts, CDA was quantified using echocardiography or Cardiac Magnetic Resonance. CDA behaves as a complex trait in the mouse cohort. IMP levels in the myocardium were associated with CDA. ipQTLs integrated into genetic models with cdaQTLs account for more CDA phenotypic variation than that explained by cda-QTLs alone. Allelic forms of genes encoding IMPs associated with CDA in mice, including AKT1, MAPK14, MAPK8, STAT3, CAS3, and TP53, are genetic determinants of CDA in patients. Two genetic risk scores for pediatric patients (n = 71) and women with breast cancer (n = 420) were generated using machine-learning Least Absolute Shrinkage and Selection Operator (LASSO) regression. Thus, IMPs associated with heart damage identify genetic markers of CDA risk, thereby allowing more personalized patient management.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

The Carbon Budget of Land Conversion: Sugarcane Expansion and Implications for a Sustainable Bioenergy Landscape in Southeastern United States

The expansion of sugarcane onto land currently occupied by improved (IMP) and semi-native (SN) pastures will reshape the U.S. bioenergy landscape. We combined biometric, ground-based and eddy covariance methods to investigate the impact of sugarcane expansion across subtropical Florida on the carbon (C) budget over a 3-year rotation. With 2.3- and 5.1-fold increase in productivity over IMP and SN pastures, sugarcane displayed a C use efficiency (CUE; i.e., fraction of gross C uptake allocated to plant growth) of 0.59, well above that of pastures (0.31–0.23). Sugarcane also had greater C allocation to aboveground productivity and hence, harvestable biomass relative to IMP and SN. Cane heterotrophic respiration over the 3-year rotation (903 ± 335 gC m −2 year −1 ) was 1% and 14% higher than IMP and SN pastures, respectively. These soil C losses responded largely to disturbance over the first year after conversion (1510 ± 227 gC m −2 year −1 ) but declined in subsequent years to an average 599 ± 90 gC m −2 year −1 —well below those of IMP (933 ± 140 gC m −2 year −1 ) and SN (759 ± 114 gC m −2 year −1 ) pastures—despite a significant 40%–61% increase in soil C inputs. Soil C inputs, however, shifted from root-dominated in pastures to litter-dominated in sugarcane, with only 5% C allocation to roots. Reduced decomposition rates in sugarcane were likely driven by changes in the recalcitrance and distribution rather than the size of the newly incorporated soil C pool. As a result, we observed a rapid shift in the net ecosystem C balance (NECB) of sugarcane from a large source immediately following conversion to approaching the net C losses of IMP pastures only 2 years after conversion. The environmental cost of converting pasture to sugarcane underscores the importance of implementing management practices to harness the soil C storage potential of sugarcane in advancing a sustainable bioeconomy in Southeastern United States.

09 BIOMASS FUELS↗
DOE OSTI2018

Large-scale Meteorological Organization of Extreme Weather Events: Final Technical Report

Although the occurrence of regional extreme weather events (EWEs) such as cold air outbreaks, heat waves, droughts and floods are known to be related to planetary climate modes (PCMs) such as the El-Nino Southern Oscillation or North Atlantic Oscillation, intermediate meteorological patterns (IMPs) such as jet stream blocking, cyclones, and high pressure systems are required to connect PCMs to EWEs. Our project has revealed a physical pathway for the interplay among EWEs, IMPs and PCMs. Under support of this award, we have characterized the behavior of IMPs that cause winter cold air outbreaks, extreme floods and warm season dry spells in the US. This includes formulating meteorological “fingerprints” for easily identifying IMPs. The research performed includes a parallel analysis of how well modern climate models are able to simulate IMP behavior. We have also developed a novel approach for characterizing PCM structures and identifying EWE-LMP-PCM linkages. We discovered that dry spells occurring during spring and summer over the US are affected by changes in the North Pacific Ocean temperature. We further revealed the physical origin of a critical jet stream pattern occurring over the North Pacific Ocean that provides a “bridge” between the water cycles of East Asia and North America, respectively. We developed an advanced diagnostic technique (called piecewise tendency diagnosis or PTD) to understand the physical causes for the IMP formation and EWE-LMP-PCM linkages.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Characterizing the X-Ray Emission of Intermediate-mass Pre-main-sequence Stars

We use X-ray and infrared observations to study the properties of three classes of young stars in the Carina Nebula: intermediate-mass (2–5 M {sub ⊙}) pre-main-sequence stars (IMPS; i.e., intermediate-mass T Tauri stars), late-B and A stars on the zero-age main sequence (AB), and lower-mass T Tauri stars (TTS). We divide our sources among these three subclassifications and further identify disk-bearing young stellar objects versus diskless sources with no detectable infrared (IR) excess emission using IR (1–8 μm) spectral energy distribution modeling. We then perform X-ray spectral fitting to determine the hydrogen-absorbing column density (N {sub H}), absorption-corrected X-ray luminosity (L {sub X}), and coronal plasma temperature (kT) for each source. We find that the X-ray spectra of both IMPS and TTS are characterized by similar kT and N {sub H}, and on average L {sub X}/L {sub bol} ~ 4 × 10{sup -4}. IMPS are systematically more luminous in X-rays (by ~0.3 dex) than all other subclassifications, with median L {sub X} = 2.5 × 10{sup 31} erg s{sup -1}, while AB stars of similar masses have X-ray emission consistent with TTS companions. These lines of evidence converge on a magnetocoronal flaring source for IMPS X-ray emission, a scaled-up version of the TTS emission mechanism. IMPS therefore provide powerful probes of isochronal ages for the first ~10 Myr in the evolution of a massive stellar population, because their intrinsic, coronal X-ray emission decays rapidly after they commence evolving along radiative tracks. We suggest that the most luminous (in both X-rays and IR) IMPS could be used to place empirical constraints on the location of the intermediate-mass stellar birth line.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Application of gas dynamical friction for planetesimals. I. Evolution of single planetesimals

The growth of small planetesimals into large planetary embryos occurs far before the dispersal of the gas from the protoplanetary disk. The planetesimal–gaseous disk interactions give rise to migration and orbital evolution of the planetesimals/planets. Small planetesimals are dominated by aerodynamic gas drag. Large protoplanets, m∼0.1M{sub ⊕}, are dominated by type I migration differential torque. There is an additional mass range m∼10{sup 21}−10{sup 25} g of intermediate-mass planetesimals (IMPs), where gravitational interactions with the disk dominate over aerodynamic gas drag, but for which such interactions were typically neglected. Here, we model these interactions using the gas dynamical friction (GDF) approach, previously used to study the disk–planet interactions at the planetary mass range. We find the critical size where GDF dominates over gas drag, and then we study the implications of GDF on single IMPs. We find that planetesimals with small inclinations rapidly become co-planar. Eccentric orbits circularize within a few Myr, provided the the planetesimal mass is large, m≳10{sup 23} g, and that the initial eccentricity is low, e≲0.1. Planetesimals of higher masses, m∼10{sup 24}−10{sup 25} g, inspiral on a timescale of a few Myr, leading to an embryonic migration to the inner disk. This can lead to an overabundance of rocky material (in the form of IMPs) in the inner protoplanetary disk (<1 AU) and induce rapid planetary growth. This can explain the origin of super-Earth planets. In addition, GDF damps the velocities of IMPs, thereby cooling the planetesimal disk and affecting its collisional evolution through quenching the effects of viscous stirring by the large bodies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Finite and infinite matrix product states for Gutzwiller projected mean-field wave functions

Matrix product states (MPS) and “dressed” ground states of quadratic mean fields (e.g., Gutzwiller projected Slater determinants) are both important classes of variational wave functions. This latter class has played important roles in understanding superconductivity and quantum spin liquids. We present a method to obtain both the finite and infinite MPS (iMPS) representation of the ground state of an arbitrary fermionic quadratic mean-field Hamiltonian (which in the simplest case is a Slater determinant and in the most general case is a Pfaffian). We also show how to represent products of such states (e.g., determinants times Pfaffians). From this representation one can project to single occupancy and evaluate the entanglement spectra after Gutzwiller projection. We then obtain the MPS and iMPS representation of Gutzwiller projected mean-field states that arise from the variational slave-fermion approach to the S = 1 bilinear-biquadratic quantum spin chain. To accomplish this, we develop an approach to orthogonalize degenerate iMPS to find all the states in the degenerate ground-state manifold. We find the energies of the MPS and iMPS states match the variational energies closely, indicating the method is accurate and there is minimal loss due to truncation error. We then present an exploration of the entanglement spectra of projected slave-fermion states, exploring their qualitative features and finding good qualitative agreement with the respective exact ground-state spectra found from density matrix renormalization group.

1-dimensional spin chains↗