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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Amino acid changes within the E protein hinge region that affect dengue virus type 2 infectivity and fusion

Fifteen mutant dengue viruses were engineered and used to identify AAs in the molecular hinge of the envelope protein that are critical to viral infection. Substitutions at Q52, A54, or E133 reduced infectivity in mammalian cells and altered the pH threshold of fusion. Mutations at F193, G266, I270, or G281 affected viral replication in mammalian and mosquito cells, but only I270W had reduced fusion activity. T280Y affected the pH threshold for fusion and reduced replication in C6/36 cells. Three different mutations at L135 were lethal in mammalian cells. Among them, L135G abrogated fusion and reduced replication in C6/36 cells, but only slightly reduced the mosquito infection rate. Conversely, L135W replicated well in C6/36 cells, but had the lowest mosquito infection rate. Possible interactions between hinge residues 52 and 277, or among 53, 135, 170, 186, 265, and 276 required for hinge function were discovered by sequence analysis to identify compensatory mutations.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Fitness Landscape-Guided Engineering of Locally Supercharged Virus-like Particles with Enhanced Cell Uptake Properties

Protein-based nanoparticles are useful models for the study of self-assembly and attractive candidates for drug delivery. Virus-like particles (VLPs) are especially promising platforms for expanding the repertoire of therapeutics that can be delivered effectively as they can deliver many copies of a molecule per particle for each delivery event. However, their use is often limited due to poor uptake of VLPs into mammalian cells. In this study, we use the fitness landscape of the bacteriophage MS2 VLP as a guide to engineer capsid variants with positively charged surface residues to enhance their uptake into mammalian cells. By combining mutations with positive fitness scores that were likely to produce assembled capsids, we identified two key double mutants with internalization efficiencies as much as 67-fold higher than that of wtMS2. Internalization of these variants with positively charged surface residues depends on interactions with cell surface sulfated proteoglycans, and yet, they are biophysically similar to wtMS2 with low cytotoxicity and an overall negative charge. Additionally, the best-performing engineered MS2 capsids can deliver a potent anticancer small-molecule therapeutic with efficacy levels similar to antibody-drug conjugates. Through this work, we were able to establish fitness landscape-based engineering as a successful method for designing VLPs with improved cell penetration. These findings suggest that VLPs with positive surface charge could be useful in improving the delivery of small-molecule- and nucleic acid-based therapeutics.

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

Inhibition of Acinetobacter -Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel β-Lactamase Inhibitors

Boronic acids are attracting a lot of attention as β-lactamase inhibitors, and in particular, compound S02030 (K i = 44 nM) proved to be a good lead compound against ADC-7 (Acinetobacter-derived cephalosporinase), one of the most significant resistance determinants in A. baumannii. The atomic structure of the ADC-7/S02030 complex highlighted the importance of critical structural determinants for recognition of the boronic acids. Herein, to elucidate the role in recognition of the R2-carboxylate, which mimics the C 3 /C 4 found in β-lactams, we designed, synthesized, and characterized six derivatives of S02030 (3a). Out of the six compounds, the best inhibitors proved to be those with an explicit negative charge (compounds 3a–c, 3h, and 3j, K i = 44–115 nM), which is in contrast to the derivatives where the negative charge is omitted, such as the amide derivative 3d (K i = 224 nM) and the hydroxyamide derivative 3e (K i = 155 nM). To develop a structural characterization of inhibitor binding in the active site, the X-ray crystal structures of ADC-7 in a complex with compounds 3c, SM23, and EC04 were determined. All three compounds share the same structural features as in S02030 but only differ in the carboxy-R2 side chain, thereby providing the opportunity of exploring the distinct binding mode of the negatively charged R2 side chain. This cephalosporinase demonstrates a high degree of versatility in recognition, employing different residues to directly interact with the carboxylate, thus suggesting the existence of a “carboxylate binding region” rather than a binding site in ADC enzymes. As a result, this class of compounds was tested against resistant clinical strains of A. baumannii and are effective at inhibiting bacterial growth in conjunction with a β-lactam antibiotic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Aerosol Vertical Turbulent Mass Flux Retrievals Through Novel Remote Sensing Algorithm

Abstract Integrated measurements of aerosol, radiation, cloud, and turbulent transport in the planetary boundary layer (PBL) are essential for understanding and modeling climate and air quality. Here, we developed a new technique for the identification of convective turbulent regions and deriving the vertical distribution of aerosol turbulent mass fluxes within PBL. The algorithm uses retrievals from coherent Doppler lidars and a high spectral resolution lidar. The technique was applied to study particle mass fluxes over 2 months (November–December 2020) during the campaign conducted at the DOE Atmospheric Radiation Measurement Southern Great Plains (SGP) site in Lamont, Oklahoma. The algorithm developed here is capable of continuously deriving vertically resolved (curtains) aerosol mass fluxes. Our data analysis shows that at the site, the 30‐min averaged fluxes at 135 m above the surface were mainly positive (upward) at ∼1 μg m −2 s −1 , suggesting that the surface is the primary source of the particle mass supplied to the boundary layer at the SGP site. Analyses of the individual case studies have revealed that not all the derived fluxes can be linked to surface emissions. Both positive and negative values in a range of ±5 μg m −2 s −1 can be caused by convective thermals interacting between the residual layer and the mixed layer and by rotation of the horizontal wind with the height. Large erroneous negative fluxes can also be caused by drizzling/precipitating clouds. We anticipate that the application of the current technique will lead to a more realistic representation of aerosol mass budgets and bidirectional mixing rates.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry

Diverse entry inhibitors targeting the gp120 subunit of the HIV-1 envelope (Env) trimer have been developed including BMS-626529, also called temsavir, a prodrug version of which is currently in phase III clinical trials. Here we report the characterization of a panel of small molecule inhibitors including BMS-818251, which we show to be >10-fold more potent than temsavir on a cross-clade panel of 208-HIV-1 strains, as well as the engineering of a crystal lattice to enable structure determination of the interaction between these inhibitors and the HIV-1 Env trimer at higher resolution. By altering crystallization lattice chaperones, we identify a lattice with both improved diffraction and robust co-crystallization of HIV-1 Env trimers from different clades complexed to entry inhibitors with a range of binding affinities. The improved diffraction reveals BMS-818251 to utilize functional groups that interact with gp120 residues from the conserved β20-β21 hairpin to improve potency.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif

Abstract The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.

Science & Technology - Other Topics↗
DOE OSTI2023

Monatomic ions influence substrate permeation across bacterial microcompartment shells

Abstract Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Influence of fluorination on CO 2 adsorption in materials derived from fluorinated covalent triazine framework precursors

Ultra-nanoporous materials derived from fluorinated covalent triazine frameworks (CTFs) have been developed for highly efficient CO 2 capture. A CO 2 uptake capacity of 6.58 mmol g –1 at 273 K, 1 bar (2.45 mmol g –1 at 0.15 bar) is achieved. The excellent performance is due to the presence of ultra-micropores (0.6–0.7 nm) that tightly fit CO 2 and strong electrostatic interactions from the residual fluorine atoms within the framework. Here, both molecular simulation and deep learning study predict that CTFs with a F content of ~4.8 wt% and pore size distribution around ~0.7 nm can give rise to the highest CO 2 uptake capacity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

The DFT+Umol method and its application to the adsorption of CO on platinum model clusters

Semi-local DFT approximations are well-known for their difficulty with describing the correct site preference for the adsorption of CO molecules on (111) surfaces of several late transition metals. To address this problem originating from a residual self-interaction in the CO LUMO, we present the DFT+Umol approach which generalizes the empirical DFT+U correction to fragment molecular orbitals. This correction is applied to examine CO adsorption energies at various sites on the (111) facets of cuboctahedral clusters Pt{sub m}(CO){sub 8} (m = 79, 140, 225). The DFT+Umol correction leaves the electronic ground state of metal clusters, in particular their d-band structure, essentially unchanged, affecting almost exclusively the energy of the CO LUMO. As a result, that correction is significantly stronger for complexes at hollow sites, hence increases the propensity for adsorption at top sites. We also analyze competing edge effects on the (111) facets of the cluster models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Peripheral positions encode transport specificity in the small multidrug resistance exporters

In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.

Science & Technology - Other Topics↗
DOE OSTI2021

Parallel molecular mechanisms for enzyme temperature adaptation

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. Furthermore, we identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Single, Double and Quadruple Alanine Substitutions at Oligomeric Interfaces Identify Hydrophobicity as the Key Determinant of Human Neutrophil Alpha Defensin HNP1 Function

HNP1 is a human alpha defensin that forms dimers and multimers governed by hydrophobic residues, including Tyr 16 , Ile 20 , Leu 25 , and Phe 28 . Previously, alanine scanning mutagenesis identified each of these residues and other hydrophobic residues as important for function. Here we report further structural and functional studies of residues shown to interact with one another across oligomeric interfaces: I20A-HNP1 and L25A-HNP1, plus the double alanine mutants I20A/L25AHNP1 and Y16A/F28A-HNP1, and the quadruple alanine mutant Y16A/I20A/L25A/F28A-HNP1. We tested binding to HIV-1 gp120 and HNP1 by surface plasmon resonance, binding to HIV-1 gp41 and HNP1 by fluorescence polarization, inhibition of anthrax lethal factor, and antibacterial activity using the virtual colony count assay. Similar to the previously described single mutant W26A-HNP1, the quadruple mutant displayed the least activity in all functional assays, followed by the double mutant Y16A/F28A-HNP1. The effects of the L25A and I20A single mutations were milder than the double mutant I20A/ L25A-HNP1. Crystallographic studies confirmed the correct folding and disulfide pairing, and depicted an array of dimeric and tetrameric structures. These results indicate that side chain hydrophobicity is the critical factor that determines activity at these positions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Special Analysis of the Area 3 Radioactive Waste Management Site at the Nevada National Security Site, Nye County, Nevada

This report describes the methods and results of a special analysis (SA) of the Area 3 Radioactive Waste Management Site (RWMS) on the Nevada National Security Site (NNSS). The purpose of the SA is to determine if the approved performance assessment (PA) and composite analysis (CA) (Shott et al., 2001) remain valid. The Area 3 RWMS PA and CA were prepared as a single document and received conditional approval on October 6, 1999. A conditional Disposal Authorization Statement (DAS) for the Area 3 RWMS was issued on October 20, 1999. Since preparation of the approved PA and CA, new information and additional environmental monitoring data have been used to update the PA and CA. At the same time, continual advancements in computer processors and software have allowed improvement to the PA and CA models. Annual reviews of the PA and CA required by U.S. Department of Energy (DOE) Order DOE O 435.1 have documented multiple changes occurring since preparation of the PA and CA. Potentially important changes include: Development of a new and improved baseline PA and CA model implemented in the probabilistic GoldSim simulation platform. A significant increase in the waste inventory disposed at the site. Revision and updating of model parameters based on additional years of site monitoring data and new research and development results. Although changes have occurred, many important PA/CA issues remain unchanged, including the site conceptual model, important features, events, and processes, and the points of compliance. The SA is performed to document the current status of the PA/CA model and to quantitatively assess the impact of cumulative changes on the PA and CA results. The results of the SA are used to assess the validity of the approved PA/CA and make a determination if revision of the PA or CA is necessary. The SA was performed using the Area 3 RWMS, version 2.102, GoldSim model, the current baseline PA/CA model. Comparison of the maximum SA results with the PA performance objectives indicates that there continues to be a reasonable expectation of compliance. The resident exposure scenario was evaluated for compliance with the air pathway and all-pathways annual total effective dose (TED) performance objectives. The maximum mean air pathway TED, 7E-6 millisievert (mSv) at 1,000 years (y) has decreased relative to the approved PA and is significantly less than the 0.1 mSv limit. The maximum mean all-pathways annual TED, 7E-5 mSv at 1,000 y has increased but remains a small fraction of the 0.25 mSv limit. The SA maximum mean radon-222 (222Rn) flux density, 0.03 becquerel per square meter per second (Bq m-2 s-1), has increased relative to the PA results but is significantly less than the 0.74 Bq m-2 s-1 limit. The SA results continue to support a conclusion that the disposed waste inventory is protective of intruders and groundwater resources. The maximum mean intruder TED, 0.01 mSv for an acute construction scenario at the U-3ah/at disposal unit, was less than the 5 mSv performance measure. Site monitoring data and research results continue to support a conclusion that a groundwater pathway will not exist within the 1,000 y compliance period. Projected releases to the environment are a small fraction of the performance objectives. Cost-effective options for reducing releases further are unlikely to exist. Therefore, releases from the Area 3 RWMS are judged to be as low as reasonably achievable. Comparison of the maximum CA result with the 0.3 mSv CA dose constraint indicates that no action is required to reduce the dose from the Area 3 RWMS and all interacting sources of residual radioactive contamination. The SA maximum mean CA annual TED, 0.02 mSv at 1,000 y, has increased from the approved CA result but remains less than 10% of the dose constraint. The CA TED continues to be due predominantly to inhalation of plutonium-239 resuspended from soils contaminated by nuclear weapons tests conducted near the Area 3 RWMS. The SA results estimated with the Area 3 RWMS version 2.102 model indicate that changes to the PA and CA do not significantly alter the PA/CA results or conclusions. Although increases occur for the all-pathways annual TED, the 222Rn flux density, and the CA annual TED, all PA and CA results are a small fraction of the performance objectives or dose constraints. The same conclusion was reached for the approved PA and CA. The SA results continue to support a conclusion that there is a reasonable expectation of meeting all performance objectives and the CA dose constraint. There is no need to revise the DAS at this time. The SA results support a conclusion that the Area 3 RWMS PA and CA remain valid, and revision is not necessary at this time.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

04BM XFM Beamline Radiation Shielding Analysis

The radiation shielding of the 04-BM-XFM beam line is analyzed for the gas bremsstrahlung (GB) and synchrotron radiation (SR) sources. The GB as a source originates from the long straight section of the storage ring during normal operation when the primary electrons interact with the residual gas molecules in the beam transport pipe giving rise to bremsstrahlung radiation. When the safety shutters are open, this can stream through the beampipe into the first optical enclosure (FOE) and beyond and can result in a radiation environment that is present at a constant rate.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural Characterization of TRAF6 N-Terminal for Therapeutic Uses and Computational Studies on New Derivatives

Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source “Turkish DeLight” to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Binary architecture of the Na v 1.2-β2 signaling complex

To investigate the mechanisms by which β-subunits influence Na v channel function, we solved the crystal structure of the β2 extracellular domain at 1.35Å. We combined these data with known bacterial Na v channel structural insights and novel functional studies to determine the interactions of specific residues in β2 with Na v 1.2. We identified a flexible loop formed by 72 Cys and 75 Cys, a unique feature among the four β-subunit isoforms. Moreover, we found that 55 Cys helps to determine the influence of β2 on Na v 1.2 toxin susceptibility. Further mutagenesis combined with the use of spider toxins reveals that 55 Cys forms a disulfide bond with 910 Cys in the Na v 1.2 domain II pore loop, thereby suggesting a 1:1 stoichiometry. Our results also provide clues as to which disulfide bonds are formed between adjacent Na v 1.2 912/918 Cys residues. The concepts emerging from this work will help to form a model reflecting the β-subunit location in a Na v channel complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

The measles virus phosphoprotein interacts with the linker domain of STAT1

The measles virus (MV) phosphoprotein (P) and V proteins block the interferon (IFN) response by impeding phosphorylation of the signal transducer and activator of transcription 1 (STAT1) by the Janus kinase 1 (JAK1). We characterized how STAT1 mutants interact with P and JAK1 phosphorylation. Certain mutants of the linker, the Src-homology 2 domain (SH2), or the transactivation domain had reduced or abolished phosphorylation through JAK1 after IFN treatment. Other mutants, mainly localized in the linker, failed to interact with P as documented by the lack of interference with nuclear translocation. Thus the functional footprint of P on STAT1 localizes mainly to the linker domain; there is also some overlap with the STAT1 phosphorylation functional footprint on the SH2 domain. Based on these observations, we discuss how the MV-P might operate to inhibit the JAK/STAT pathway. - Highlights: • Residue in the linker and SH2 domains of STAT1 are important for MV-P interaction. • Residue in the linker and SH2 domains of STAT1 are important for STAT1 phosphorylation. • Residues interferring with both functions have similar location on STAT1. • The viral P and V proteins may operate in concert to inhibit the JAK/STAT pathway.

60 APPLIED LIFE SCIENCES↗